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yh202109 committed Jul 25, 2024
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12 changes: 8 additions & 4 deletions _modules/mtbp3/stdcdisc/lib.html
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Expand Up @@ -283,21 +283,25 @@ <h1>Source code for mtbp3.stdcdisc.lib</h1><div class="highlight"><pre>
<span class="n">remaining_list_label</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">codelists</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
<span class="k">if</span> <span class="s1">&#39;conceptId&#39;</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span> <span class="ow">and</span> <span class="s1">&#39;name&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">item</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span><span class="o">=</span><span class="s2">&quot;&quot;</span>
<span class="k">if</span> <span class="s1">&#39;group&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">item</span><span class="p">[</span><span class="s1">&#39;group&#39;</span><span class="p">]</span><span class="o">=</span><span class="s2">&quot;&quot;</span>
<span class="k">if</span> <span class="s1">&#39;synonyms&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">item</span><span class="p">[</span><span class="s1">&#39;synonyms&#39;</span><span class="p">]</span><span class="o">=</span><span class="p">[]</span>
<span class="k">if</span> <span class="s1">&#39;terms&#39;</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">keys</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">item</span><span class="p">[</span><span class="s1">&#39;terms&#39;</span><span class="p">])):</span>
<span class="k">if</span> <span class="s1">&#39;name&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;terms&#39;</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">item</span><span class="p">[</span><span class="s1">&#39;terms&#39;</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="s1">&#39;name&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="n">item</span><span class="p">[</span><span class="s1">&#39;terms&#39;</span><span class="p">][</span><span class="n">i</span><span class="p">][</span><span class="s1">&#39;group&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span>
<span class="n">nterms</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="s1">&#39;terms&#39;</span><span class="p">])</span>
<span class="n">remaining_list</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="s1">&#39;terms&#39;</span><span class="p">])</span>
<span class="n">remaining_list_label</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="n">codelists_label</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">+</span><span class="s1">&#39;.pseudo&#39;</span><span class="o">+</span><span class="n">item</span><span class="p">[</span><span class="s1">&#39;conceptId&#39;</span><span class="p">]]</span><span class="o">*</span><span class="n">nterms</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">nterms</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">codelists_label</span><span class="p">[</span><span class="n">index</span><span class="p">],</span> <span class="n">level</span><span class="p">,</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;conceptId&#39;</span><span class="p">],</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">],</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;preferredTerm&#39;</span><span class="p">],</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;submissionValue&#39;</span><span class="p">],</span> <span class="s1">&#39;; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="s1">&#39;synonyms&#39;</span><span class="p">]),</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;definition&#39;</span><span class="p">],</span> <span class="n">nterms</span><span class="p">])</span>
<span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">codelists_label</span><span class="p">[</span><span class="n">index</span><span class="p">],</span> <span class="n">level</span><span class="p">,</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;conceptId&#39;</span><span class="p">],</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">],</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;group&#39;</span><span class="p">],</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;preferredTerm&#39;</span><span class="p">],</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;submissionValue&#39;</span><span class="p">],</span> <span class="s1">&#39;; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="s1">&#39;synonyms&#39;</span><span class="p">]),</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;definition&#39;</span><span class="p">],</span> <span class="n">nterms</span><span class="p">])</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">not_processed</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>

<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">,</span> <span class="s1">&#39;level&#39;</span><span class="p">,</span> <span class="s1">&#39;conceptId&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">,</span> <span class="s1">&#39;preferredTerm&#39;</span><span class="p">,</span> <span class="s1">&#39;submissionValue&#39;</span><span class="p">,</span> <span class="s1">&#39;synonyms&#39;</span><span class="p">,</span> <span class="s1">&#39;definition&#39;</span><span class="p">,</span> <span class="s1">&#39;terms&#39;</span><span class="p">])</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">,</span> <span class="s1">&#39;level&#39;</span><span class="p">,</span> <span class="s1">&#39;conceptId&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">,</span> <span class="s1">&#39;group&#39;</span><span class="p">,</span> <span class="s1">&#39;preferredTerm&#39;</span><span class="p">,</span> <span class="s1">&#39;submissionValue&#39;</span><span class="p">,</span> <span class="s1">&#39;synonyms&#39;</span><span class="p">,</span> <span class="s1">&#39;definition&#39;</span><span class="p">,</span> <span class="s1">&#39;terms&#39;</span><span class="p">])</span>
<span class="n">label</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s1">&#39;label&#39;</span><span class="p">,</span> <span class="s1">&#39;preferredTerm&#39;</span><span class="p">]]</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s1">&#39;label&#39;</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>

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32 changes: 29 additions & 3 deletions _sources/std_cdisc.ipynb.txt
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"cell_type": "markdown",
"metadata": {},
"source": [
"To get the newest protocol ct package information:\n",
"To get the newest Protocol CT package in DataFrame format:\n",
"\n",
"```python\n",
"title = 'Protocol'\n",
"cl = accessLib(\"/Users/yh2020/cdisc.txt\")\n",
"from mtbp3.stdcdisc.lib import accessLib\n",
"cl = accessLib(\"/user/home/name/cdisc.txt\")\n",
"cl.get_ct_list()\n",
"title = 'Protocol'\n",
"cl.get_ct_package(title)\n",
"cl.get_ct_codelists_df(title)\n",
"print(cl.ct_package[title]['ct_df'][['conceptId', 'name', 'preferredTerm']].head())\n",
Expand All @@ -249,6 +250,31 @@
"```"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"To get the newest Glossary CT package in DataFrame format:\n",
"\n",
"```python\n",
"title = 'Glossary'\n",
"cl.get_ct_package(title)\n",
"cl.get_ct_codelists_df(title)\n",
"print(cl.ct_package[title]['ct_df'][['conceptId', 'name', 'group', 'preferredTerm', 'definition']].head())\n",
"```\n",
"\n",
"Output:\n",
"\n",
"```\n",
" conceptId name group preferredTerm definition\n",
"0 C67497 CDISC Glossary CDISC Glossary Terminology The terminology of the Clinical Data Interchan...\n",
"1 C80442 CDISC Glossary Premarket Device Notification 510(k). Premarket Notification (PMN) required ...\n",
"2 C42610 CDISC Glossary Abbreviation A set of letters that are drawn from a word or...\n",
"3 C71733 CDISC Glossary Biological Absorption The process by which medications reach the blo...\n",
"4 C156638 CDISC Glossary Accelerated Approval Regulatory mechanism by which new drugs meant ...\n",
"```"
]
},
{
"cell_type": "markdown",
"metadata": {},
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14 changes: 9 additions & 5 deletions _static/reports/coverage/coverage.xml
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