Deploying to gh-pages from @ 9537006 🚀

latest/_modules/phenopacket_mapper/mapping/mapper.html

@@ -110,15 +110,11 @@ <h1>Source code for phenopacket_mapper.mapping.mapper</h1><div class="highlight"
         <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">check_data_fields_in_model</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
 
-
-<div class="viewcode-block" id="PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values">
-<a class="viewcode-back" href="../../../apidocs/phenopacket_mapper.mapping.mapper.html#phenopacket_mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values">[docs]</a>
-    <span class="k">def</span> <span class="nf">check_fields_adheres_to_phenopacket_allowed_values</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Check if the fields in the mapping adhere to the values in the Phenopacket schema</span>
-
-<span class="sd">        Check the Phenopacket schema to see if the fields in the mapping adhere to the values allowed by the schema.</span>
-<span class="sd">        Otherwise give precise error messages.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
+    <span class="c1"># TODO: implement check_fields_adheres_to_phenopacket_allowed_values</span>
+
+<div class="viewcode-block" id="PhenopacketMapper.check_data_fields_in_model">
+<a class="viewcode-back" href="../../../apidocs/phenopacket_mapper.mapping.mapper.html#phenopacket_mapper.PhenopacketMapper.check_data_fields_in_model">[docs]</a>
+    <span class="k">def</span> <span class="nf">check_data_fields_in_model</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">element</span><span class="p">):</span>
         <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">element</span><span class="p">,</span> <span class="n">DataField</span><span class="p">):</span>
             <span class="n">field</span> <span class="o">=</span> <span class="n">element</span>
             <span class="k">if</span> <span class="n">field</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_model</span><span class="p">:</span>
@@ -162,7 +158,6 @@ <h1>Source code for phenopacket_mapper.mapping.mapper</h1><div class="highlight"
         <span class="k">return</span> <span class="n">phenopackets_list</span></div>
 </div>
 
-
 </pre></div>
 
            </div>

latest/apidocs/phenopacket_mapper.html

@@ -65,7 +65,7 @@
 </ul>
 </li>
 <li class="toctree-l3"><a class="reference internal" href="#phenopacket_mapper.PhenopacketMapper"><code class="docutils literal notranslate"><span class="pre">PhenopacketMapper</span></code></a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#phenopacket_mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values"><code class="docutils literal notranslate"><span class="pre">PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#phenopacket_mapper.PhenopacketMapper.check_data_fields_in_model"><code class="docutils literal notranslate"><span class="pre">PhenopacketMapper.check_data_fields_in_model()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#phenopacket_mapper.PhenopacketMapper.map"><code class="docutils literal notranslate"><span class="pre">PhenopacketMapper.map()</span></code></a></li>
 </ul>
 </li>
@@ -211,12 +211,9 @@
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.</span></span><span class="sig-name descname"><span class="pre">PhenopacketMapper</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.html#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/mapping/mapper.html#PhenopacketMapper"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.PhenopacketMapper" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <dl class="py method">
-<dt class="sig sig-object py" id="phenopacket_mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values">
-<span class="sig-name descname"><span class="pre">check_fields_adheres_to_phenopacket_allowed_values</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/mapping/mapper.html#PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values" title="Link to this definition"></a></dt>
-<dd><p>Check if the fields in the mapping adhere to the values in the Phenopacket schema</p>
-<p>Check the Phenopacket schema to see if the fields in the mapping adhere to the values allowed by the schema.
-Otherwise give precise error messages.</p>
-</dd></dl>
+<dt class="sig sig-object py" id="phenopacket_mapper.PhenopacketMapper.check_data_fields_in_model">
+<span class="sig-name descname"><span class="pre">check_data_fields_in_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/mapping/mapper.html#PhenopacketMapper.check_data_fields_in_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.PhenopacketMapper.check_data_fields_in_model" title="Link to this definition"></a></dt>
+<dd></dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="phenopacket_mapper.PhenopacketMapper.map">

latest/apidocs/phenopacket_mapper.mapping.html

@@ -119,12 +119,9 @@
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.mapping.</span></span><span class="sig-name descname"><span class="pre">PhenopacketMapper</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.html#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/mapping/mapper.html#PhenopacketMapper"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.mapping.PhenopacketMapper" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <dl class="py method">
-<dt class="sig sig-object py" id="phenopacket_mapper.mapping.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values">
-<span class="sig-name descname"><span class="pre">check_fields_adheres_to_phenopacket_allowed_values</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/mapping/mapper.html#PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.mapping.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values" title="Link to this definition"></a></dt>
-<dd><p>Check if the fields in the mapping adhere to the values in the Phenopacket schema</p>
-<p>Check the Phenopacket schema to see if the fields in the mapping adhere to the values allowed by the schema.
-Otherwise give precise error messages.</p>
-</dd></dl>
+<dt class="sig sig-object py" id="phenopacket_mapper.mapping.PhenopacketMapper.check_data_fields_in_model">
+<span class="sig-name descname"><span class="pre">check_data_fields_in_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/mapping/mapper.html#PhenopacketMapper.check_data_fields_in_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.mapping.PhenopacketMapper.check_data_fields_in_model" title="Link to this definition"></a></dt>
+<dd></dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="phenopacket_mapper.mapping.PhenopacketMapper.map">

latest/apidocs/phenopacket_mapper.mapping.mapper.html

@@ -83,12 +83,9 @@
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.mapping.mapper.</span></span><span class="sig-name descname"><span class="pre">PhenopacketMapper</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.html#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/mapping/mapper.html#PhenopacketMapper"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.mapping.mapper.PhenopacketMapper" title="Link to this definition"></a></dt>
 <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <dl class="py method">
-<dt class="sig sig-object py" id="phenopacket_mapper.mapping.mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values">
-<span class="sig-name descname"><span class="pre">check_fields_adheres_to_phenopacket_allowed_values</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/mapping/mapper.html#PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.mapping.mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values" title="Link to this definition"></a></dt>
-<dd><p>Check if the fields in the mapping adhere to the values in the Phenopacket schema</p>
-<p>Check the Phenopacket schema to see if the fields in the mapping adhere to the values allowed by the schema.
-Otherwise give precise error messages.</p>
-</dd></dl>
+<dt class="sig sig-object py" id="phenopacket_mapper.mapping.mapper.PhenopacketMapper.check_data_fields_in_model">
+<span class="sig-name descname"><span class="pre">check_data_fields_in_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/mapping/mapper.html#PhenopacketMapper.check_data_fields_in_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.mapping.mapper.PhenopacketMapper.check_data_fields_in_model" title="Link to this definition"></a></dt>
+<dd></dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="phenopacket_mapper.mapping.mapper.PhenopacketMapper.map">

latest/genindex.html

@@ -160,12 +160,12 @@ <h2 id="C">C</h2>
         <li><a href="apidocs/phenopacket_mapper.data_standards.html#phenopacket_mapper.data_standards.OrGroup.cardinality">(phenopacket_mapper.data_standards.OrGroup attribute)</a>
 </li>
       </ul></li>
-      <li><a href="apidocs/phenopacket_mapper.mapping.mapper.html#phenopacket_mapper.mapping.mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values">check_fields_adheres_to_phenopacket_allowed_values() (phenopacket_mapper.mapping.mapper.PhenopacketMapper method)</a>
+      <li><a href="apidocs/phenopacket_mapper.mapping.mapper.html#phenopacket_mapper.mapping.mapper.PhenopacketMapper.check_data_fields_in_model">check_data_fields_in_model() (phenopacket_mapper.mapping.mapper.PhenopacketMapper method)</a>
 
       <ul>
-        <li><a href="apidocs/phenopacket_mapper.mapping.html#phenopacket_mapper.mapping.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values">(phenopacket_mapper.mapping.PhenopacketMapper method)</a>
+        <li><a href="apidocs/phenopacket_mapper.mapping.html#phenopacket_mapper.mapping.PhenopacketMapper.check_data_fields_in_model">(phenopacket_mapper.mapping.PhenopacketMapper method)</a>
 </li>
-        <li><a href="apidocs/phenopacket_mapper.html#phenopacket_mapper.PhenopacketMapper.check_fields_adheres_to_phenopacket_allowed_values">(phenopacket_mapper.PhenopacketMapper method)</a>
+        <li><a href="apidocs/phenopacket_mapper.html#phenopacket_mapper.PhenopacketMapper.check_data_fields_in_model">(phenopacket_mapper.PhenopacketMapper method)</a>
 </li>
       </ul></li>
   </ul></td>