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latest/_modules/phenopacket_mapper/data_standards/data_model.html

@@ -88,7 +88,7 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class=
 
 <span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span><span class="p">,</span> <span class="n">field</span>
 <span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span>
-<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Callable</span><span class="p">,</span> <span class="n">Tuple</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Callable</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Iterable</span>
 <span class="kn">import</span> <span class="nn">warnings</span>
 
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
@@ -648,6 +648,34 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class=
                 <span class="k">return</span> <span class="n">f</span>
         <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;&#39;OrGroup&#39; object has no attribute &#39;</span><span class="si">{</span><span class="n">var_name</span><span class="si">}</span><span class="s2">&#39;&quot;</span><span class="p">)</span></div>
 
+
+
+<div class="viewcode-block" id="recursive_collect_all_members_data_model">
+<a class="viewcode-back" href="../../../apidocs/phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.recursive_collect_all_members_data_model">[docs]</a>
+<span class="k">def</span> <span class="nf">recursive_collect_all_members_data_model</span><span class="p">(</span>
+        <span class="n">data_model</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">DataModel</span><span class="p">,</span> <span class="n">DataSection</span><span class="p">,</span> <span class="n">OrGroup</span><span class="p">,</span> <span class="n">DataField</span><span class="p">]</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Iterable</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="n">DataSection</span><span class="p">,</span> <span class="n">OrGroup</span><span class="p">,</span> <span class="n">DataField</span><span class="p">]]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Recursively collect all members of a DataModel, DataSection, OrGroup, or DataField</span>
+
+<span class="sd">    :param data_model: DataModel, DataSection, OrGroup, or DataField to collect all members from</span>
+<span class="sd">    :return: Iterable of DataSection, OrGroup, and DataField members</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data_model</span><span class="p">,</span> <span class="n">DataModel</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">data_model</span><span class="o">.</span><span class="n">fields</span><span class="p">:</span>
+            <span class="k">yield from</span> <span class="n">recursive_collect_all_members_data_model</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data_model</span><span class="p">,</span> <span class="n">DataSection</span><span class="p">):</span>
+        <span class="k">yield</span> <span class="n">data_model</span>
+        <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">data_model</span><span class="o">.</span><span class="n">fields</span><span class="p">:</span>
+            <span class="k">yield from</span> <span class="n">recursive_collect_all_members_data_model</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data_model</span><span class="p">,</span> <span class="n">OrGroup</span><span class="p">):</span>
+        <span class="k">yield</span> <span class="n">data_model</span>
+        <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">data_model</span><span class="o">.</span><span class="n">fields</span><span class="p">:</span>
+            <span class="k">yield from</span> <span class="n">recursive_collect_all_members_data_model</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data_model</span><span class="p">,</span> <span class="n">DataField</span><span class="p">):</span>
+        <span class="k">yield</span> <span class="n">data_model</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Unsupported data_model type: </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="n">data_model</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span></div>
+
 </pre></div>
 
            </div>

latest/apidocs/phenopacket_mapper.data_standards.data_model.html

@@ -542,6 +542,20 @@
 
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.data_model.recursive_collect_all_members_data_model">
+<span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.data_standards.data_model.</span></span><span class="sig-name descname"><span class="pre">recursive_collect_all_members_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="#phenopacket_mapper.data_standards.data_model.DataSection" title="phenopacket_mapper.data_standards.data_model.DataSection"><span class="pre">DataSection</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="#phenopacket_mapper.data_standards.data_model.OrGroup" title="phenopacket_mapper.data_standards.data_model.OrGroup"><span class="pre">OrGroup</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="#phenopacket_mapper.data_standards.data_model.DataField" title="phenopacket_mapper.data_standards.data_model.DataField"><span class="pre">DataField</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.Iterable" title="(in Python v3.13)"><span class="pre">Iterable</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#phenopacket_mapper.data_standards.data_model.DataSection" title="phenopacket_mapper.data_standards.data_model.DataSection"><span class="pre">DataSection</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="#phenopacket_mapper.data_standards.data_model.OrGroup" title="phenopacket_mapper.data_standards.data_model.OrGroup"><span class="pre">OrGroup</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="#phenopacket_mapper.data_standards.data_model.DataField" title="phenopacket_mapper.data_standards.data_model.DataField"><span class="pre">DataField</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/data_model.html#recursive_collect_all_members_data_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.recursive_collect_all_members_data_model" title="Link to this definition"></a></dt>
+<dd><p>Recursively collect all members of a DataModel, DataSection, OrGroup, or DataField</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>data_model</strong> – DataModel, DataSection, OrGroup, or DataField to collect all members from</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Iterable of DataSection, OrGroup, and DataField members</p>
+</dd>
+</dl>
+</dd></dl>
+
 </section>
 
 

latest/apidocs/phenopacket_mapper.data_standards.html

@@ -1013,6 +1013,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <li class="toctree-l2"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataModelInstance"><code class="docutils literal notranslate"><span class="pre">DataModelInstance</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataSet"><code class="docutils literal notranslate"><span class="pre">DataSet</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.OrGroup"><code class="docutils literal notranslate"><span class="pre">OrGroup</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.recursive_collect_all_members_data_model"><code class="docutils literal notranslate"><span class="pre">recursive_collect_all_members_data_model()</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="phenopacket_mapper.data_standards.date.html">phenopacket_mapper.data_standards.date module</a><ul>

latest/genindex.html

@@ -1339,6 +1339,8 @@ <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.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.recursive_collect_all_members_data_model">recursive_collect_all_members_data_model() (in module phenopacket_mapper.data_standards.data_model)</a>
+</li>
       <li><a href="apidocs/phenopacket_mapper.utils.html#phenopacket_mapper.utils.recursive_dict_call">recursive_dict_call() (in module phenopacket_mapper.utils)</a>
 
       <ul>