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latest/_modules/phenopacket_mapper/data_standards/code_system.html

@@ -142,13 +142,13 @@ <h1>Source code for phenopacket_mapper.data_standards.code_system</h1><div class
 <span class="n">GENO</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
     <span class="n">name</span><span class="o">=</span><span class="s1">&#39;GENO: The Genotype Ontology&#39;</span><span class="p">,</span> 
     <span class="n">namespace_prefix</span><span class="o">=</span><span class="s1">&#39;GENO&#39;</span><span class="p">,</span> 
-    <span class="n">url</span><span class="o">=</span><span class="s1">&#39;http://www.genoontology.org/&#39;</span>
+    <span class="n">url</span><span class="o">=</span><span class="s1">&#39;https://www.genoontology.org/&#39;</span>
 <span class="p">)</span>
 
 <span class="n">SO</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
     <span class="n">name</span><span class="o">=</span><span class="s1">&#39;Sequence types and features ontology&#39;</span><span class="p">,</span> 
     <span class="n">namespace_prefix</span><span class="o">=</span><span class="s1">&#39;SO&#39;</span><span class="p">,</span>
-    <span class="n">url</span><span class="o">=</span><span class="s1">&#39;http://www.sequenceontology.org/&#39;</span>
+    <span class="n">url</span><span class="o">=</span><span class="s1">&#39;https://www.sequenceontology.org/&#39;</span>
 <span class="p">)</span>
 
 <span class="n">ICD9</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
@@ -212,12 +212,12 @@ <h1>Source code for phenopacket_mapper.data_standards.code_system</h1><div class
 <span class="n">MONDO</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
     <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Monarch Disease Ontology&quot;</span><span class="p">,</span>
     <span class="n">namespace_prefix</span><span class="o">=</span><span class="s2">&quot;MONDO&quot;</span><span class="p">,</span>
-    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;http://purl.obolibrary.org/obo/mondo.owl&quot;</span>
+    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;https://purl.obolibrary.org/obo/mondo.owl&quot;</span>
 <span class="p">)</span>
 <span class="n">ORDO</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
     <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Orphanet Rare Disease Ontology&quot;</span><span class="p">,</span>
     <span class="n">namespace_prefix</span><span class="o">=</span><span class="s2">&quot;ORPHA&quot;</span><span class="p">,</span>
-    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;http://www.orpha.net/&quot;</span><span class="p">,</span>
+    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;https://www.orpha.net/&quot;</span><span class="p">,</span>
     <span class="n">synonyms</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;ORDO&#39;</span><span class="p">]</span>
 <span class="p">)</span>
 <span class="n">OMIM</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
@@ -233,7 +233,7 @@ <h1>Source code for phenopacket_mapper.data_standards.code_system</h1><div class
 <span class="n">HGVS</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
     <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Human Genome Variation Society&quot;</span><span class="p">,</span>
     <span class="n">namespace_prefix</span><span class="o">=</span><span class="s2">&quot;HGVS&quot;</span><span class="p">,</span>
-    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;http://varnomen.hgvs.org/&quot;</span>
+    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;https://varnomen.hgvs.org/&quot;</span>
 <span class="p">)</span>
 <span class="n">HGNC</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
     <span class="n">name</span><span class="o">=</span><span class="s2">&quot;HUGO Gene Nomenclature Committee&quot;</span><span class="p">,</span>
@@ -243,14 +243,14 @@ <h1>Source code for phenopacket_mapper.data_standards.code_system</h1><div class
 <span class="n">HPO</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
     <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Human Phenotype Ontology&quot;</span><span class="p">,</span>
     <span class="n">namespace_prefix</span><span class="o">=</span><span class="s2">&quot;HP&quot;</span><span class="p">,</span>
-    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;http://www.human-phenotype-ontology.org&quot;</span><span class="p">,</span>
-    <span class="n">iri_prefix</span><span class="o">=</span><span class="s2">&quot;http://purl.obolibrary.org/obo/HP_&quot;</span><span class="p">,</span>
+    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;https://www.human-phenotype-ontology.org&quot;</span><span class="p">,</span>
+    <span class="n">iri_prefix</span><span class="o">=</span><span class="s2">&quot;https://purl.obolibrary.org/obo/HP_&quot;</span><span class="p">,</span>
     <span class="n">synonyms</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;HPO&quot;</span><span class="p">]</span>
 <span class="p">)</span>
 <span class="n">UO</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
     <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Units of Measurement Ontology&quot;</span><span class="p">,</span>
     <span class="n">namespace_prefix</span><span class="o">=</span><span class="s2">&quot;UO&quot;</span><span class="p">,</span>
-    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;http://www.ontobee.org/ontology/UO&quot;</span>
+    <span class="n">url</span><span class="o">=</span><span class="s2">&quot;https://www.ontobee.org/ontology/UO&quot;</span>
 <span class="p">)</span>
 <span class="n">NCIT</span> <span class="o">=</span> <span class="n">CodeSystem</span><span class="p">(</span>
     <span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;NCI Thesaurus OBO Edition&quot;</span><span class="p">,</span>

latest/_modules/phenopacket_mapper/data_standards/data_model.html

@@ -240,7 +240,7 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class=
 <span class="sd">    :ivar resources: List of `CodeSystem` objects</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">data_model_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">field</span><span class="p">()</span>
-    <span class="n">fields</span><span class="p">:</span> <span class="n">Tuple</span><span class="p">[</span><span class="n">DataField</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">()</span>
+    <span class="n">fields</span><span class="p">:</span> <span class="n">Tuple</span><span class="p">[</span><span class="n">DataField</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">()</span>
     <span class="n">resources</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">CodeSystem</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -255,8 +255,8 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class=
 
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="n">ret</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;DataModel(name=</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">data_model_name</span><span class="si">}</span><span class="se">\n</span><span class="s2">&quot;</span>
-        <span class="k">for</span> <span class="n">field</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">fields</span><span class="p">:</span>
-            <span class="n">ret</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="se">\t</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">field</span><span class="p">)</span><span class="si">}</span><span class="se">\n</span><span class="s2">&quot;</span>
+        <span class="k">for</span> <span class="n">_field</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">fields</span><span class="p">:</span>
+            <span class="n">ret</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="se">\t</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">_field</span><span class="p">)</span><span class="si">}</span><span class="se">\n</span><span class="s2">&quot;</span>
         <span class="n">ret</span> <span class="o">+=</span> <span class="s2">&quot;---</span><span class="se">\n</span><span class="s2">&quot;</span>
         <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">resources</span><span class="p">:</span>
             <span class="n">ret</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="se">\t</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">)</span><span class="si">}</span><span class="se">\n</span><span class="s2">&quot;</span>
@@ -512,11 +512,12 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class=
         <span class="k">for</span> <span class="n">instance</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
             <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_model</span><span class="o">.</span><span class="n">fields</span><span class="p">:</span>
                 <span class="n">field_id</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">id</span>
+                <span class="n">value</span><span class="p">:</span> <span class="n">Any</span> <span class="o">=</span> <span class="kc">None</span>
                 <span class="k">try</span><span class="p">:</span>
                     <span class="n">dfv</span><span class="p">:</span> <span class="n">DataFieldValue</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">instance</span><span class="p">,</span> <span class="n">field_id</span><span class="p">)</span>
                     <span class="n">value</span> <span class="o">=</span> <span class="n">dfv</span><span class="o">.</span><span class="n">value</span>
                 <span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
-                    <span class="n">value</span> <span class="o">=</span> <span class="kc">None</span>
+                    <span class="k">pass</span>
                 <span class="k">finally</span><span class="p">:</span>
                     <span class="n">data_dict</span><span class="p">[</span><span class="n">field_id</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data_dict</span><span class="p">,</span> <span class="n">columns</span><span class="o">=</span><span class="n">column_names</span><span class="p">)</span>

latest/_modules/phenopacket_mapper/pipeline/input.html

@@ -80,7 +80,7 @@ <h1>Source code for phenopacket_mapper.pipeline.input</h1><div class="highlight"
 <span class="kn">import</span> <span class="nn">os</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">types</span> <span class="kn">import</span> <span class="n">MappingProxyType</span>
-<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Dict</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Tuple</span>
 
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 <span class="kn">from</span> <span class="nn">phenopackets.schema.v2</span> <span class="kn">import</span> <span class="n">Phenopacket</span>
@@ -174,7 +174,7 @@ <h1>Source code for phenopacket_mapper.pipeline.input</h1><div class="highlight"
             <span class="k">return</span> <span class="n">value</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39; &#39;</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">value</span>
 
-    <span class="n">data_fields</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">data_fields</span><span class="p">:</span> <span class="n">Tuple</span><span class="p">[</span><span class="n">DataField</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">()</span>
     <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">)):</span>
         <span class="n">data_field_name</span> <span class="o">=</span> <span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">))</span>
         <span class="n">section</span> <span class="o">=</span> <span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">section</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">))</span>
@@ -203,7 +203,7 @@ <h1>Source code for phenopacket_mapper.pipeline.input</h1><div class="highlight"
                 <span class="n">resources</span><span class="o">=</span><span class="n">resources</span>
             <span class="p">)</span>
 
-        <span class="n">data_fields</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+        <span class="n">data_fields</span> <span class="o">=</span> <span class="n">data_fields</span> <span class="o">+</span> <span class="p">(</span>
             <span class="n">DataField</span><span class="p">(</span>
                 <span class="n">name</span><span class="o">=</span><span class="n">data_field_name</span><span class="p">,</span>
                 <span class="n">section</span><span class="o">=</span><span class="n">section</span><span class="p">,</span>
@@ -212,7 +212,7 @@ <h1>Source code for phenopacket_mapper.pipeline.input</h1><div class="highlight"
                 <span class="n">required</span><span class="o">=</span><span class="n">required</span><span class="p">,</span>
                 <span class="n">specification</span><span class="o">=</span><span class="n">specification</span><span class="p">,</span>
                 <span class="n">ordinal</span><span class="o">=</span><span class="n">ordinal</span>
-            <span class="p">)</span>
+            <span class="p">),</span>
         <span class="p">)</span>
 
     <span class="k">return</span> <span class="n">DataModel</span><span class="p">(</span><span class="n">data_model_name</span><span class="o">=</span><span class="n">data_model_name</span><span class="p">,</span> <span class="n">fields</span><span class="o">=</span><span class="n">data_fields</span><span class="p">,</span> <span class="n">resources</span><span class="o">=</span><span class="n">resources</span><span class="p">)</span></div>

latest/_modules/phenopacket_mapper/utils/create_ipynb_in_code.html

@@ -85,8 +85,6 @@ <h1>Source code for phenopacket_mapper.utils.create_ipynb_in_code</h1><div class
 <span class="k">class</span> <span class="nc">NotebookBuilder</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    A class to build a Jupyter notebook programmatically.</span>
-
-<span class="sd">    :param notebook_content: A dictionary representing the notebook structure.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -177,7 +175,7 @@ <h1>Source code for phenopacket_mapper.utils.create_ipynb_in_code</h1><div class
     <span class="n">builder</span><span class="o">.</span><span class="n">add_code_cell</span><span class="p">(</span><span class="s2">&quot;x = np.linspace(0, 10, 100)</span><span class="se">\n</span><span class="s2">print(x)&quot;</span><span class="p">)</span>
     <span class="n">builder</span><span class="o">.</span><span class="n">add_markdown_cell</span><span class="p">(</span><span class="s2">&quot;## Analysis&quot;</span><span class="p">)</span>
     <span class="n">builder</span><span class="o">.</span><span class="n">add_code_cell</span><span class="p">(</span><span class="s2">&quot;y = np.sin(x)</span><span class="se">\n</span><span class="s2">print(y)&quot;</span><span class="p">)</span>
-    <span class="n">builder</span><span class="o">.</span><span class="n">write_to_file</span><span class="p">(</span><span class="s1">&#39;my_notebook.ipynb&#39;</span><span class="p">)</span>
+    <span class="n">builder</span><span class="o">.</span><span class="n">write_to_file</span><span class="p">(</span><span class="n">Path</span><span class="p">(</span><span class="s1">&#39;my_notebook.ipynb&#39;</span><span class="p">))</span>
 </pre></div>
 
            </div>