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latest/_modules/phenopacket_mapper/utils/io/read_xml.html

@@ -136,13 +136,33 @@ <h1>Source code for phenopacket_mapper.utils.io.read_xml</h1><div class="highlig
     <span class="k">return</span> <span class="n">dict_</span>
 
 
+<div class="viewcode-block" id="remove_at_symbols">
+<a class="viewcode-back" href="../../../../apidocs/phenopacket_mapper.utils.io.read_xml.html#phenopacket_mapper.utils.io.remove_at_symbols">[docs]</a>
+<span class="k">def</span> <span class="nf">remove_at_symbols</span><span class="p">(</span><span class="n">dict_</span><span class="p">:</span> <span class="n">Dict</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">:</span>
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dict_</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+        <span class="n">new_dict</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">dict_</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+            <span class="k">if</span> <span class="n">k</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;@&quot;</span><span class="p">):</span>
+                <span class="n">k</span> <span class="o">=</span> <span class="n">k</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+                <span class="n">new_dict</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">remove_at_symbols</span><span class="p">(</span><span class="n">item</span><span class="p">)</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">v</span><span class="p">]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">new_dict</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">remove_at_symbols</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new_dict</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">dict_</span></div>
+
+
+
 <div class="viewcode-block" id="parse_xml">
 <a class="viewcode-back" href="../../../../apidocs/phenopacket_mapper.utils.io.read_xml.html#phenopacket_mapper.utils.io.parse_xml">[docs]</a>
 <span class="k">def</span> <span class="nf">parse_xml</span><span class="p">(</span><span class="n">file</span><span class="p">:</span> <span class="n">IOBase</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Parse an XML file into a dictionary with inferred types.&quot;&quot;&quot;</span>
     <span class="n">dict_</span> <span class="o">=</span> <span class="n">xmltodict</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">file</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
     <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">dict_</span><span class="si">=}</span><span class="s2">, </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="n">dict_</span><span class="p">)</span><span class="si">=}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="n">dict_</span> <span class="o">=</span> <span class="n">_post_process_xml_dict</span><span class="p">(</span><span class="n">dict_</span><span class="p">)</span>
+    <span class="n">dict_</span> <span class="o">=</span> <span class="n">remove_at_symbols</span><span class="p">(</span><span class="n">dict_</span><span class="p">)</span>
     <span class="k">return</span> <span class="n">dict_</span></div>
 
 

latest/apidocs/phenopacket_mapper.utils.io.html

@@ -231,6 +231,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 </li>
 <li class="toctree-l1"><a class="reference internal" href="phenopacket_mapper.utils.io.read_xml.html">phenopacket_mapper.utils.io.read_xml module</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="phenopacket_mapper.utils.io.read_xml.html#phenopacket_mapper.utils.io.read_xml.read_xml"><code class="docutils literal notranslate"><span class="pre">read_xml()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="phenopacket_mapper.utils.io.read_xml.html#phenopacket_mapper.utils.io.read_xml.remove_at_symbols"><code class="docutils literal notranslate"><span class="pre">remove_at_symbols()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="phenopacket_mapper.utils.io.read_xml.html#phenopacket_mapper.utils.io.read_xml.parse_xml"><code class="docutils literal notranslate"><span class="pre">parse_xml()</span></code></a></li>
 </ul>
 </li>

latest/apidocs/phenopacket_mapper.utils.io.read_xml.html

@@ -83,6 +83,11 @@
 <span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.utils.io.read_xml.</span></span><span class="sig-name descname"><span class="pre">read_xml</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.13)"><span class="pre">Path</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/io.html#io.IOBase" title="(in Python v3.13)"><span class="pre">IOBase</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">encoding</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'utf-8'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/utils/io/read_xml.html#read_xml"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.utils.io.read_xml.read_xml" title="Link to this definition"></a></dt>
 <dd></dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="phenopacket_mapper.utils.io.read_xml.remove_at_symbols">
+<span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.utils.io.read_xml.</span></span><span class="sig-name descname"><span class="pre">remove_at_symbols</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dict_</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/utils/io/read_xml.html#remove_at_symbols"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.utils.io.read_xml.remove_at_symbols" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="phenopacket_mapper.utils.io.read_xml.parse_xml">
 <span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.utils.io.read_xml.</span></span><span class="sig-name descname"><span class="pre">parse_xml</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/io.html#io.IOBase" title="(in Python v3.13)"><span class="pre">IOBase</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/utils/io/read_xml.html#parse_xml"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.utils.io.read_xml.parse_xml" title="Link to this definition"></a></dt>

latest/genindex.html

@@ -1304,6 +1304,8 @@ <h2 id="R">R</h2>
         <li><a href="apidocs/phenopacket_mapper.utils.io.read_xml.html#phenopacket_mapper.utils.io.read_xml.read_xml">(in module phenopacket_mapper.utils.io.read_xml)</a>
 </li>
       </ul></li>
+      <li><a href="apidocs/phenopacket_mapper.utils.io.read_xml.html#phenopacket_mapper.utils.io.read_xml.remove_at_symbols">remove_at_symbols() (in module phenopacket_mapper.utils.io.read_xml)</a>
+</li>
       <li><a href="apidocs/phenopacket_mapper.data_standards.value_set.html#phenopacket_mapper.data_standards.value_set.ValueSet.remove_duplicates">remove_duplicates() (phenopacket_mapper.data_standards.value_set.ValueSet method)</a>
 
       <ul>