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_modules/pandasaurus_cxg/anndata_analyzer.html

@@ -258,7 +258,7 @@ <h1>Source code for pandasaurus_cxg.anndata_analyzer</h1><div class="highlight">
     <span class="k">def</span> <span class="nf">_enrich_co_annotation</span><span class="p">(</span><span class="n">enricher</span><span class="p">:</span> <span class="n">AnndataEnricher</span><span class="p">):</span>
         <span class="n">enriched_df</span> <span class="o">=</span> <span class="n">enricher</span><span class="o">.</span><span class="n">enricher</span><span class="o">.</span><span class="n">enriched_df</span>
         <span class="k">if</span> <span class="n">enriched_df</span><span class="o">.</span><span class="n">empty</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="k">return</span> <span class="n">enriched_df</span>
         <span class="k">return</span> <span class="n">enriched_df</span><span class="p">[</span><span class="n">enriched_df</span><span class="p">[</span><span class="s2">&quot;o&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">enricher</span><span class="o">.</span><span class="n">seed_list</span><span class="p">)][[</span><span class="s2">&quot;s_label&quot;</span><span class="p">,</span> <span class="s2">&quot;o_label&quot;</span><span class="p">]]</span>
 
     <span class="k">def</span> <span class="nf">_filter_data_and_drop_duplicates</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">field_name_1</span><span class="p">,</span> <span class="n">field_name_2</span><span class="p">,</span> <span class="n">disease</span><span class="p">):</span>

_modules/pandasaurus_cxg/graph_generator/graph_generator.html

@@ -83,6 +83,7 @@ <h1>Source code for pandasaurus_cxg.graph_generator.graph_generator</h1><div cla
 <span class="kn">from</span> <span class="nn">rdflib.plugins.sparql</span> <span class="kn">import</span> <span class="n">prepareQuery</span>
 
 <span class="kn">from</span> <span class="nn">pandasaurus_cxg.enrichment_analysis</span> <span class="kn">import</span> <span class="p">(</span>
+    <span class="n">AnndataAnalyzer</span><span class="p">,</span>
     <span class="n">AnndataEnricher</span><span class="p">,</span>
     <span class="n">AnndataEnrichmentAnalyzer</span><span class="p">,</span>
 <span class="p">)</span>
@@ -102,6 +103,7 @@ <h1>Source code for pandasaurus_cxg.graph_generator.graph_generator</h1><div cla
 <span class="p">)</span>
 <span class="kn">from</span> <span class="nn">pandasaurus_cxg.utils.exceptions</span> <span class="kn">import</span> <span class="p">(</span>
     <span class="n">InvalidGraphFormat</span><span class="p">,</span>
+    <span class="n">MissingAnalysisProcess</span><span class="p">,</span>
     <span class="n">MissingEnrichmentProcess</span><span class="p">,</span>
 <span class="p">)</span>
 <span class="kn">from</span> <span class="nn">pandasaurus_cxg.utils.logging_config</span> <span class="kn">import</span> <span class="n">configure_logger</span>
@@ -130,6 +132,10 @@ <h1>Source code for pandasaurus_cxg.graph_generator.graph_generator</h1><div cla
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="c1"># TODO need to think about how to handle the requirement of enrichment and co_annotation_analysis methods</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">ea</span> <span class="o">=</span> <span class="n">enrichment_analyzer</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ea</span><span class="o">.</span><span class="n">analyzer_manager</span><span class="o">.</span><span class="n">report_df</span><span class="o">.</span><span class="n">empty</span><span class="p">:</span>
+            <span class="n">analysis_methods</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">dir</span><span class="p">(</span><span class="n">AnndataAnalyzer</span><span class="p">)</span> <span class="k">if</span> <span class="s2">&quot;_report&quot;</span> <span class="ow">in</span> <span class="n">i</span><span class="p">]</span>
+            <span class="n">analysis_methods</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
+            <span class="k">raise</span> <span class="n">MissingAnalysisProcess</span><span class="p">(</span><span class="n">analysis_methods</span><span class="p">)</span>
         <span class="c1"># TODO need to handle invalid keys. We also need to discuss about keeping the keys param. DO NOT USE</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="p">(</span>
             <span class="n">enrichment_analyzer</span><span class="o">.</span><span class="n">analyzer_manager</span><span class="o">.</span><span class="n">report_df</span><span class="p">[</span><span class="n">keys</span><span class="p">]</span>

_modules/pandasaurus_cxg/utils/exceptions.html

@@ -116,14 +116,25 @@ <h1>Source code for pandasaurus_cxg.utils.exceptions</h1><div class="highlight">
 <span class="k">class</span> <span class="nc">MissingEnrichmentProcess</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">enrichment_methods</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">message</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="sa">f</span><span class="s2">&quot;Any of the following enrichment methods from AnndataEnricher must be used before &quot;</span>
-            <span class="sa">f</span><span class="s2">&quot;using enriched_rdf_graph method: &quot;</span>
+            <span class="sa">f</span><span class="s2">&quot;Any of the following enrichment methods from AnndataEnricher must be used first; &quot;</span>
             <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">enrichment_methods</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span>
         <span class="p">)</span>
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">message</span><span class="p">)</span></div>
 
 
 
+<div class="viewcode-block" id="MissingAnalysisProcess">
+<a class="viewcode-back" href="../../../pandasaurus_cxg/utils/exception.html#pandasaurus_cxg.utils.exceptions.MissingAnalysisProcess">[docs]</a>
+<span class="k">class</span> <span class="nc">MissingAnalysisProcess</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">analysis_methods</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">message</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="sa">f</span><span class="s2">&quot;Any of the following analysis methods from AnndataAnalyser must be used first; &quot;</span>
+            <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">analysis_methods</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span>
+        <span class="p">)</span>
+        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">message</span><span class="p">)</span></div>
+
+
+
 <div class="viewcode-block" id="SubclassWarning">
 <a class="viewcode-back" href="../../../pandasaurus_cxg/utils/exception.html#pandasaurus_cxg.utils.exceptions.SubclassWarning">[docs]</a>
 <span class="k">class</span> <span class="nc">SubclassWarning</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>

genindex.html

@@ -232,10 +232,12 @@ <h2 id="M">M</h2>
         <li><a href="pandasaurus_cxg/enrichment_analysis.html#pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer.minimal_slim_enrichment">(pandasaurus_cxg.enrichment_analysis.AnndataEnrichmentAnalyzer method)</a>
 </li>
       </ul></li>
-      <li><a href="pandasaurus_cxg/utils/exception.html#pandasaurus_cxg.utils.exceptions.MissingEnrichmentProcess">MissingEnrichmentProcess</a>
+      <li><a href="pandasaurus_cxg/utils/exception.html#pandasaurus_cxg.utils.exceptions.MissingAnalysisProcess">MissingAnalysisProcess</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="pandasaurus_cxg/utils/exception.html#pandasaurus_cxg.utils.exceptions.MissingEnrichmentProcess">MissingEnrichmentProcess</a>
+</li>
       <li>
     module
 

pandasaurus_cxg/utils/exception.html

@@ -111,6 +111,12 @@ <h1>Exception Module<a class="headerlink" href="#exception-module" title="Link t
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
 </dd></dl>
 
+<dl class="py exception">
+<dt class="sig sig-object py" id="pandasaurus_cxg.utils.exceptions.MissingAnalysisProcess">
+<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pandasaurus_cxg.utils.exceptions.</span></span><span class="sig-name descname"><span class="pre">MissingAnalysisProcess</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analysis_methods</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/pandasaurus_cxg/utils/exceptions.html#MissingAnalysisProcess"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pandasaurus_cxg.utils.exceptions.MissingAnalysisProcess" title="Link to this definition"></a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
+</dd></dl>
+
 <dl class="py exception">
 <dt class="sig sig-object py" id="pandasaurus_cxg.utils.exceptions.MissingEnrichmentProcess">
 <em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pandasaurus_cxg.utils.exceptions.</span></span><span class="sig-name descname"><span class="pre">MissingEnrichmentProcess</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">enrichment_methods</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/pandasaurus_cxg/utils/exceptions.html#MissingEnrichmentProcess"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pandasaurus_cxg.utils.exceptions.MissingEnrichmentProcess" title="Link to this definition"></a></dt>