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INCATools · Jul 12, 2024 · 9c92c4f · 9c92c4f
1 parent 80dc323
commit 9c92c4f
Showing 1 changed file with 16 additions and 12 deletions.
diff --git a/_modules/pandasaurus_cxg/graph_generator/graph_generator.html b/_modules/pandasaurus_cxg/graph_generator/graph_generator.html
@@ -320,6 +320,14 @@ <h1>Source code for pandasaurus_cxg.graph_generator.graph_generator</h1><div cla
         <span class="n">percentage_annotation_property</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ns</span><span class="p">[</span><span class="s2">&quot;percentage&quot;</span><span class="p">]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">add</span><span class="p">((</span><span class="n">percentage_annotation_property</span><span class="p">,</span> <span class="n">RDF</span><span class="o">.</span><span class="n">type</span><span class="p">,</span> <span class="n">OWL</span><span class="o">.</span><span class="n">AnnotationProperty</span><span class="p">))</span>
         <span class="k">for</span> <span class="n">metadata</span> <span class="ow">in</span> <span class="n">metadata_fields</span><span class="p">:</span>
+            <span class="c1"># Extract the ontology term ID mapping</span>
+            <span class="n">ontology_term_id_mapping</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">obs</span><span class="p">[[</span><span class="n">metadata</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">metadata</span><span class="si">}</span><span class="s2">_ontology_term_id&quot;</span><span class="p">]]</span>
+                <span class="o">.</span><span class="n">drop_duplicates</span><span class="p">()</span>
+                <span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="n">metadata</span><span class="p">)</span>
+                <span class="o">.</span><span class="n">to_dict</span><span class="p">()[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">metadata</span><span class="si">}</span><span class="s2">_ontology_term_id&quot;</span><span class="p">]</span>
+            <span class="p">)</span>
+
             <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">_</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">triples</span><span class="p">((</span><span class="kc">None</span><span class="p">,</span> <span class="n">RDF</span><span class="o">.</span><span class="n">type</span><span class="p">,</span> <span class="n">URIRef</span><span class="p">(</span><span class="n">CLUSTER</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;iri&quot;</span><span class="p">)))):</span>
                 <span class="k">for</span> <span class="n">a_cell_type</span> <span class="ow">in</span> <span class="n">author_cell_types</span><span class="p">:</span>
                     <span class="n">literal</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">value</span><span class="p">(</span><span class="n">subject</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">predicate</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ns</span><span class="p">[</span><span class="n">a_cell_type</span><span class="p">])</span>
@@ -330,19 +338,15 @@ <h1>Source code for pandasaurus_cxg.graph_generator.graph_generator</h1><div cla
                         <span class="o">*</span> <span class="mi">100</span>
                     <span class="p">)</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span> <span class="o">!=</span> <span class="mf">0.0</span><span class="p">]</span>
 
-                    <span class="c1"># Extract the ontology term ID mapping</span>
-                    <span class="n">ontology_term_id_mapping</span> <span class="o">=</span> <span class="p">(</span>
-                        <span class="n">obs</span><span class="p">[[</span><span class="n">metadata</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">metadata</span><span class="si">}</span><span class="s2">_ontology_term_id&quot;</span><span class="p">]]</span>
-                        <span class="o">.</span><span class="n">drop_duplicates</span><span class="p">()</span>
-                        <span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="n">metadata</span><span class="p">)</span>
-                        <span class="o">.</span><span class="n">to_dict</span><span class="p">()[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">metadata</span><span class="si">}</span><span class="s2">_ontology_term_id&quot;</span><span class="p">]</span>
-                    <span class="p">)</span>
-
                     <span class="k">for</span> <span class="n">label</span><span class="p">,</span> <span class="n">percentage</span> <span class="ow">in</span> <span class="n">percentages</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
-                        <span class="n">ontology_term_id</span> <span class="o">=</span> <span class="n">ontology_term_id_mapping</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">label</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;:&quot;</span><span class="p">)</span>
-                        <span class="n">annotated_target</span> <span class="o">=</span> <span class="n">Namespace</span><span class="p">(</span><span class="n">prefixes</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">ontology_term_id</span><span class="p">[</span><span class="mi">0</span><span class="p">]))[</span>
-                            <span class="n">ontology_term_id</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
-                        <span class="p">]</span>
+                        <span class="n">ontology_term_id</span> <span class="o">=</span> <span class="n">ontology_term_id_mapping</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">label</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">ontology_term_id</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span> <span class="s2">&quot;:&quot;</span> <span class="ow">in</span> <span class="n">ontology_term_id</span><span class="p">:</span>
+                            <span class="n">ontology_term_id</span> <span class="o">=</span> <span class="n">ontology_term_id_mapping</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">label</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;:&quot;</span><span class="p">)</span>
+                            <span class="n">annotated_target</span> <span class="o">=</span> <span class="n">Namespace</span><span class="p">(</span><span class="n">prefixes</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">ontology_term_id</span><span class="p">[</span><span class="mi">0</span><span class="p">]))[</span>
+                                <span class="n">ontology_term_id</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+                            <span class="p">]</span>
+                        <span class="k">else</span><span class="p">:</span>
+                            <span class="n">annotated_target</span> <span class="o">=</span> <span class="n">URIRef</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ns</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">uuid</span><span class="o">.</span><span class="n">uuid4</span><span class="p">())])</span>
                         <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">add</span><span class="p">((</span><span class="n">annotated_target</span><span class="p">,</span> <span class="n">RDFS</span><span class="o">.</span><span class="n">label</span><span class="p">,</span> <span class="n">Literal</span><span class="p">(</span><span class="n">label</span><span class="p">)))</span>
                         <span class="n">bnode_axiom</span> <span class="o">=</span> <span class="n">BNode</span><span class="p">()</span>
                         <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">add</span><span class="p">((</span><span class="n">bnode_axiom</span><span class="p">,</span> <span class="n">RDF</span><span class="o">.</span><span class="n">type</span><span class="p">,</span> <span class="n">OWL</span><span class="o">.</span><span class="n">Axiom</span><span class="p">))</span>