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yh202109 committed Jul 28, 2024
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4 changes: 2 additions & 2 deletions _downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html
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392 changes: 193 additions & 199 deletions _downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml
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3 changes: 1 addition & 2 deletions _modules/index.html
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Expand Up @@ -91,7 +91,6 @@
<div itemprop="articleBody">

<h1>All modules for which code is available</h1>
<ul><li><a href="mtbp3.html">mtbp3</a></li>
<ul><li><a href="mtbp3/health/clinical.html">mtbp3.health.clinical</a></li>
<li><a href="mtbp3/health/ectd.html">mtbp3.health.ectd</a></li>
<li><a href="mtbp3/health/emt.html">mtbp3.health.emt</a></li>
Expand All @@ -104,7 +103,7 @@ <h1>All modules for which code is available</h1>
<li><a href="mtbp3/util/cdtg.html">mtbp3.util.cdtg</a></li>
<li><a href="mtbp3/util/lsr.html">mtbp3.util.lsr</a></li>
<li><a href="mtbp3/util/util.html">mtbp3.util.util</a></li>
</ul></ul></ul>
</ul></ul>

</div>
</div>
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1 change: 0 additions & 1 deletion _modules/mtbp3/health/clinical.html
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<ul class="wy-breadcrumbs">
<li><a href="../../../index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item"><a href="../../index.html">Module code</a></li>
<li class="breadcrumb-item"><a href="../../mtbp3.html">mtbp3</a></li>
<li class="breadcrumb-item active">mtbp3.health.clinical</li>
<li class="wy-breadcrumbs-aside">
</li>
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10 changes: 4 additions & 6 deletions _modules/mtbp3/health/ectd.html
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Expand Up @@ -82,7 +82,6 @@
<ul class="wy-breadcrumbs">
<li><a href="../../../index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item"><a href="../../index.html">Module code</a></li>
<li class="breadcrumb-item"><a href="../../mtbp3.html">mtbp3</a></li>
<li class="breadcrumb-item active">mtbp3.health.ectd</li>
<li class="wy-breadcrumbs-aside">
</li>
Expand Down Expand Up @@ -110,7 +109,6 @@ <h1>Source code for mtbp3.health.ectd</h1><div class="highlight"><pre>

<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">mtbp3</span>
<span class="kn">from</span> <span class="nn">mtbp3</span> <span class="kn">import</span> <span class="n">util</span>

<div class="viewcode-block" id="ctoc_by_fda">
Expand All @@ -121,7 +119,7 @@ <h1>Source code for mtbp3.health.ectd</h1><div class="highlight"><pre>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">ctoc_version</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">all</span><span class="p">(</span><span class="n">char</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span> <span class="ow">or</span> <span class="n">char</span> <span class="o">==</span> <span class="s1">&#39;.&#39;</span> <span class="k">for</span> <span class="n">char</span> <span class="ow">in</span> <span class="n">ctoc_version</span><span class="p">),</span> <span class="s2">&quot;Version must be a string with integers and dots&quot;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ectd_version</span> <span class="o">=</span> <span class="n">ectd_version</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ctoc_version</span> <span class="o">=</span> <span class="n">ctoc_version</span>
<span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">get_data</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;supp_ectd/fda_ectd</span><span class="si">{</span><span class="n">ectd_version</span><span class="si">}</span><span class="s1">_ctocv</span><span class="si">{</span><span class="n">ctoc_version</span><span class="si">}</span><span class="s1">.txt&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">get_data</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;supp_ectd/fda_ectd</span><span class="si">{</span><span class="n">ectd_version</span><span class="si">}</span><span class="s1">_ctocv</span><span class="si">{</span><span class="n">ctoc_version</span><span class="si">}</span><span class="s1">.txt&#39;</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">ctoc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__load_list</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">folder_name</span><span class="p">)</span>

Expand All @@ -144,7 +142,7 @@ <h1>Source code for mtbp3.health.ectd</h1><div class="highlight"><pre>
<span class="n">module</span> <span class="o">=</span> <span class="mi">1</span>

<span class="n">filtered_ctoc</span> <span class="o">=</span> <span class="p">[</span><span class="n">item</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ctoc</span> <span class="k">if</span> <span class="n">item</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">module</span><span class="p">))]</span>
<span class="n">tree</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">filtered_ctoc</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
<span class="n">tree</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">filtered_ctoc</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="n">tree</span><span class="o">.</span><span class="n">list_tree</span><span class="p">(</span><span class="n">to_right</span><span class="o">=</span><span class="n">to_right</span><span class="p">)</span></div>


Expand Down Expand Up @@ -216,9 +214,9 @@ <h1>Source code for mtbp3.health.ectd</h1><div class="highlight"><pre>
<span class="n">out_colored</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">first_part</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">colored_second_part</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">out_colored</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">row</span><span class="p">)</span>
<span class="n">out_tree</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">out_colored</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
<span class="n">out_tree</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">out_colored</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">out_tree</span> <span class="o">=</span> <span class="n">mtbp3</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">out</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
<span class="n">out_tree</span> <span class="o">=</span> <span class="n">util</span><span class="o">.</span><span class="n">cdt</span><span class="o">.</span><span class="n">ListTree</span><span class="p">(</span><span class="n">lst</span><span class="o">=</span><span class="n">out</span><span class="p">,</span> <span class="n">infmt</span><span class="o">=</span><span class="s1">&#39;dotspace&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="n">out_tree</span><span class="o">.</span><span class="n">list_tree</span><span class="p">(</span><span class="n">to_right</span><span class="o">=</span><span class="n">to_right</span><span class="p">)</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="s2">&quot;Invalid value for outfmt. Supported values are &#39;simple&#39; and &#39;tree&#39;.&quot;</span><span class="p">)</span></div>
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