diff --git a/docs/api/acmc/logging_config.html b/docs/api/acmc/logging_config.html
index a844e4d8294181d98be83eff2c6a61e5f6d98680..9c9e3b90560fe8269d23aa20c6ad7b097effc9f9 100644
--- a/docs/api/acmc/logging_config.html
+++ b/docs/api/acmc/logging_config.html
@@ -55,57 +55,76 @@
                     <h1 class="modulename">
 <a href="./../acmc.html">acmc</a><wbr>.logging_config    </h1>
 
-                
+                        <div class="docstring"><p>logging_config.py</p>
+
+<p>This module defines functions to setup logging for acmc across all module. </p>
+
+<p>Constants</p>
+
+<ul>
+<li>DEFAULT_LOG_FILE: The default acmc application log filename.</li>
+</ul>
+</div>
+
                         <input id="mod-logging_config-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
 
                         <label class="view-source-button" for="mod-logging_config-view-source"><span>View Source</span></label>
 
-                        <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
-</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
+                        <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="sd">logging_config.py</span>
 </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a>
-</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="n">DEFAULT_LOG_FILE</span> <span class="o">=</span> <span class="s2">&quot;acmc.log&quot;</span>
+</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="sd">This module defines functions to setup logging for acmc across all module. </span>
 </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a>
-</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
-</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="k">def</span><span class="w"> </span><span class="nf">setup_logger</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">):</span>
-</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Sets up logger as a singleton outputing to file and sysout syserr&quot;&quot;&quot;</span>
-</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a>    <span class="c1"># Create a logger</span>
-</span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a>    <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">&quot;acmc_logger&quot;</span><span class="p">)</span>
-</span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
-</span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a>
-</span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">logger</span><span class="o">.</span><span class="n">hasHandlers</span><span class="p">():</span>
-</span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a>        <span class="c1"># Create a file handler that logs to a file</span>
-</span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a>        <span class="n">file_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">FileHandler</span><span class="p">(</span><span class="n">DEFAULT_LOG_FILE</span><span class="p">)</span>
-</span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a>        <span class="n">file_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
-</span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a>
-</span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a>        <span class="c1"># Create a stream handler that prints to the console</span>
-</span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a>        <span class="n">stream_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">()</span>
-</span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a>        <span class="n">stream_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
-</span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a>
-</span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a>        <span class="c1"># Create a formatter for how the log messages should look</span>
-</span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a>
-</span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a>        <span class="c1"># Add the formatter to both handlers</span>
-</span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a>        <span class="n">file_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span>
-</span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a>            <span class="s2">&quot;</span><span class="si">%(asctime)s</span><span class="s2"> - - </span><span class="si">%(levelname)s</span><span class="s2"> - </span><span class="si">%(message)s</span><span class="s2">&quot;</span>
-</span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a>        <span class="p">)</span>
-</span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a>        <span class="n">file_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">file_formatter</span><span class="p">)</span>
-</span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a>        <span class="n">stream_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s2">&quot;[</span><span class="si">%(levelname)s</span><span class="s2">] - </span><span class="si">%(message)s</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a>        <span class="n">stream_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">stream_formatter</span><span class="p">)</span>
+</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="sd">Constants</span>
+</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="sd">- DEFAULT_LOG_FILE: The default acmc application log filename.</span>
+</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a>
+</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a>
+</span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
+</span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
+</span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a>
+</span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a><span class="n">DEFAULT_LOG_FILE</span> <span class="o">=</span> <span class="s2">&quot;acmc.log&quot;</span> <span class="c1"># default log filename</span>
+</span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a>
+</span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a><span class="k">def</span><span class="w"> </span><span class="nf">setup_logger</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">):</span>
+</span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Sets up acmc logger as a singleton outputing to file and sysout syserr.&quot;&quot;&quot;</span>
+</span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a>    
+</span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a>    <span class="c1"># Create a logger</span>
+</span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a>    <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">&quot;acmc_logger&quot;</span><span class="p">)</span>
+</span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a>
+</span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">logger</span><span class="o">.</span><span class="n">hasHandlers</span><span class="p">():</span>
+</span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a>        <span class="c1"># Create a file handler that logs to a file</span>
+</span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a>        <span class="n">file_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">FileHandler</span><span class="p">(</span><span class="n">DEFAULT_LOG_FILE</span><span class="p">)</span>
+</span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a>        <span class="n">file_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a>
+</span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a>        <span class="c1"># Create a stream handler that prints to the console</span>
+</span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a>        <span class="n">stream_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">()</span>
+</span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a>        <span class="n">stream_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
 </span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a>
-</span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a>        <span class="c1"># Add the handlers to the logger</span>
-</span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">file_handler</span><span class="p">)</span>
-</span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">stream_handler</span><span class="p">)</span>
-</span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a>
-</span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a>    <span class="k">return</span> <span class="n">logger</span>
-</span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a>
-</span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a>
-</span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a><span class="k">def</span><span class="w"> </span><span class="nf">set_log_level</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
-</span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Sets the log level for the acmc logger&quot;&quot;&quot;</span>
-</span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a>    <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">&quot;acmc_logger&quot;</span><span class="p">)</span>
-</span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>  <span class="c1"># Set logger level</span>
-</span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a>
-</span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a>    <span class="c1"># Also update handlers to match the new level</span>
-</span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a>    <span class="k">for</span> <span class="n">handler</span> <span class="ow">in</span> <span class="n">logger</span><span class="o">.</span><span class="n">handlers</span><span class="p">:</span>
-</span><span id="L-46"><a href="#L-46"><span class="linenos">46</span></a>        <span class="n">handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>
+</span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a>        <span class="c1"># Create a formatter for how the log messages should look</span>
+</span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a>        <span class="c1"># Add the formatter to both handlers</span>
+</span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a>        <span class="n">file_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span>
+</span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a>            <span class="s2">&quot;</span><span class="si">%(asctime)s</span><span class="s2"> - - </span><span class="si">%(levelname)s</span><span class="s2"> - </span><span class="si">%(message)s</span><span class="s2">&quot;</span>
+</span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a>        <span class="p">)</span>
+</span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a>        <span class="n">file_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">file_formatter</span><span class="p">)</span>
+</span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a>        <span class="n">stream_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s2">&quot;[</span><span class="si">%(levelname)s</span><span class="s2">] - </span><span class="si">%(message)s</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a>        <span class="n">stream_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">stream_formatter</span><span class="p">)</span>
+</span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a>
+</span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a>        <span class="c1"># Add the handlers to the logger</span>
+</span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">file_handler</span><span class="p">)</span>
+</span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">stream_handler</span><span class="p">)</span>
+</span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a>
+</span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a>    <span class="k">return</span> <span class="n">logger</span>
+</span><span id="L-46"><a href="#L-46"><span class="linenos">46</span></a>
+</span><span id="L-47"><a href="#L-47"><span class="linenos">47</span></a>
+</span><span id="L-48"><a href="#L-48"><span class="linenos">48</span></a><span class="k">def</span><span class="w"> </span><span class="nf">set_log_level</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
+</span><span id="L-49"><a href="#L-49"><span class="linenos">49</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Sets the log level for the acmc logger.&quot;&quot;&quot;</span>
+</span><span id="L-50"><a href="#L-50"><span class="linenos">50</span></a>    <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">&quot;acmc_logger&quot;</span><span class="p">)</span>
+</span><span id="L-51"><a href="#L-51"><span class="linenos">51</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>
+</span><span id="L-52"><a href="#L-52"><span class="linenos">52</span></a>
+</span><span id="L-53"><a href="#L-53"><span class="linenos">53</span></a>    <span class="c1"># Also update handlers to match the new level</span>
+</span><span id="L-54"><a href="#L-54"><span class="linenos">54</span></a>    <span class="k">for</span> <span class="n">handler</span> <span class="ow">in</span> <span class="n">logger</span><span class="o">.</span><span class="n">handlers</span><span class="p">:</span>
+</span><span id="L-55"><a href="#L-55"><span class="linenos">55</span></a>        <span class="n">handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>
 </span></pre></div>
 
 
@@ -133,40 +152,40 @@
 
     </div>
     <a class="headerlink" href="#setup_logger"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="setup_logger-8"><a href="#setup_logger-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">setup_logger</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">):</span>
-</span><span id="setup_logger-9"><a href="#setup_logger-9"><span class="linenos"> 9</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Sets up logger as a singleton outputing to file and sysout syserr&quot;&quot;&quot;</span>
-</span><span id="setup_logger-10"><a href="#setup_logger-10"><span class="linenos">10</span></a>    <span class="c1"># Create a logger</span>
-</span><span id="setup_logger-11"><a href="#setup_logger-11"><span class="linenos">11</span></a>    <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">&quot;acmc_logger&quot;</span><span class="p">)</span>
-</span><span id="setup_logger-12"><a href="#setup_logger-12"><span class="linenos">12</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
-</span><span id="setup_logger-13"><a href="#setup_logger-13"><span class="linenos">13</span></a>
-</span><span id="setup_logger-14"><a href="#setup_logger-14"><span class="linenos">14</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">logger</span><span class="o">.</span><span class="n">hasHandlers</span><span class="p">():</span>
-</span><span id="setup_logger-15"><a href="#setup_logger-15"><span class="linenos">15</span></a>        <span class="c1"># Create a file handler that logs to a file</span>
-</span><span id="setup_logger-16"><a href="#setup_logger-16"><span class="linenos">16</span></a>        <span class="n">file_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">FileHandler</span><span class="p">(</span><span class="n">DEFAULT_LOG_FILE</span><span class="p">)</span>
-</span><span id="setup_logger-17"><a href="#setup_logger-17"><span class="linenos">17</span></a>        <span class="n">file_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
-</span><span id="setup_logger-18"><a href="#setup_logger-18"><span class="linenos">18</span></a>
-</span><span id="setup_logger-19"><a href="#setup_logger-19"><span class="linenos">19</span></a>        <span class="c1"># Create a stream handler that prints to the console</span>
-</span><span id="setup_logger-20"><a href="#setup_logger-20"><span class="linenos">20</span></a>        <span class="n">stream_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">()</span>
-</span><span id="setup_logger-21"><a href="#setup_logger-21"><span class="linenos">21</span></a>        <span class="n">stream_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
-</span><span id="setup_logger-22"><a href="#setup_logger-22"><span class="linenos">22</span></a>
-</span><span id="setup_logger-23"><a href="#setup_logger-23"><span class="linenos">23</span></a>        <span class="c1"># Create a formatter for how the log messages should look</span>
-</span><span id="setup_logger-24"><a href="#setup_logger-24"><span class="linenos">24</span></a>
-</span><span id="setup_logger-25"><a href="#setup_logger-25"><span class="linenos">25</span></a>        <span class="c1"># Add the formatter to both handlers</span>
-</span><span id="setup_logger-26"><a href="#setup_logger-26"><span class="linenos">26</span></a>        <span class="n">file_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span>
-</span><span id="setup_logger-27"><a href="#setup_logger-27"><span class="linenos">27</span></a>            <span class="s2">&quot;</span><span class="si">%(asctime)s</span><span class="s2"> - - </span><span class="si">%(levelname)s</span><span class="s2"> - </span><span class="si">%(message)s</span><span class="s2">&quot;</span>
-</span><span id="setup_logger-28"><a href="#setup_logger-28"><span class="linenos">28</span></a>        <span class="p">)</span>
-</span><span id="setup_logger-29"><a href="#setup_logger-29"><span class="linenos">29</span></a>        <span class="n">file_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">file_formatter</span><span class="p">)</span>
-</span><span id="setup_logger-30"><a href="#setup_logger-30"><span class="linenos">30</span></a>        <span class="n">stream_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s2">&quot;[</span><span class="si">%(levelname)s</span><span class="s2">] - </span><span class="si">%(message)s</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="setup_logger-31"><a href="#setup_logger-31"><span class="linenos">31</span></a>        <span class="n">stream_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">stream_formatter</span><span class="p">)</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="setup_logger-17"><a href="#setup_logger-17"><span class="linenos">17</span></a><span class="k">def</span><span class="w"> </span><span class="nf">setup_logger</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">):</span>
+</span><span id="setup_logger-18"><a href="#setup_logger-18"><span class="linenos">18</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Sets up acmc logger as a singleton outputing to file and sysout syserr.&quot;&quot;&quot;</span>
+</span><span id="setup_logger-19"><a href="#setup_logger-19"><span class="linenos">19</span></a>    
+</span><span id="setup_logger-20"><a href="#setup_logger-20"><span class="linenos">20</span></a>    <span class="c1"># Create a logger</span>
+</span><span id="setup_logger-21"><a href="#setup_logger-21"><span class="linenos">21</span></a>    <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">&quot;acmc_logger&quot;</span><span class="p">)</span>
+</span><span id="setup_logger-22"><a href="#setup_logger-22"><span class="linenos">22</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="setup_logger-23"><a href="#setup_logger-23"><span class="linenos">23</span></a>
+</span><span id="setup_logger-24"><a href="#setup_logger-24"><span class="linenos">24</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">logger</span><span class="o">.</span><span class="n">hasHandlers</span><span class="p">():</span>
+</span><span id="setup_logger-25"><a href="#setup_logger-25"><span class="linenos">25</span></a>        <span class="c1"># Create a file handler that logs to a file</span>
+</span><span id="setup_logger-26"><a href="#setup_logger-26"><span class="linenos">26</span></a>        <span class="n">file_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">FileHandler</span><span class="p">(</span><span class="n">DEFAULT_LOG_FILE</span><span class="p">)</span>
+</span><span id="setup_logger-27"><a href="#setup_logger-27"><span class="linenos">27</span></a>        <span class="n">file_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="setup_logger-28"><a href="#setup_logger-28"><span class="linenos">28</span></a>
+</span><span id="setup_logger-29"><a href="#setup_logger-29"><span class="linenos">29</span></a>        <span class="c1"># Create a stream handler that prints to the console</span>
+</span><span id="setup_logger-30"><a href="#setup_logger-30"><span class="linenos">30</span></a>        <span class="n">stream_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">()</span>
+</span><span id="setup_logger-31"><a href="#setup_logger-31"><span class="linenos">31</span></a>        <span class="n">stream_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
 </span><span id="setup_logger-32"><a href="#setup_logger-32"><span class="linenos">32</span></a>
-</span><span id="setup_logger-33"><a href="#setup_logger-33"><span class="linenos">33</span></a>        <span class="c1"># Add the handlers to the logger</span>
-</span><span id="setup_logger-34"><a href="#setup_logger-34"><span class="linenos">34</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">file_handler</span><span class="p">)</span>
-</span><span id="setup_logger-35"><a href="#setup_logger-35"><span class="linenos">35</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">stream_handler</span><span class="p">)</span>
-</span><span id="setup_logger-36"><a href="#setup_logger-36"><span class="linenos">36</span></a>
-</span><span id="setup_logger-37"><a href="#setup_logger-37"><span class="linenos">37</span></a>    <span class="k">return</span> <span class="n">logger</span>
+</span><span id="setup_logger-33"><a href="#setup_logger-33"><span class="linenos">33</span></a>        <span class="c1"># Create a formatter for how the log messages should look</span>
+</span><span id="setup_logger-34"><a href="#setup_logger-34"><span class="linenos">34</span></a>        <span class="c1"># Add the formatter to both handlers</span>
+</span><span id="setup_logger-35"><a href="#setup_logger-35"><span class="linenos">35</span></a>        <span class="n">file_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span>
+</span><span id="setup_logger-36"><a href="#setup_logger-36"><span class="linenos">36</span></a>            <span class="s2">&quot;</span><span class="si">%(asctime)s</span><span class="s2"> - - </span><span class="si">%(levelname)s</span><span class="s2"> - </span><span class="si">%(message)s</span><span class="s2">&quot;</span>
+</span><span id="setup_logger-37"><a href="#setup_logger-37"><span class="linenos">37</span></a>        <span class="p">)</span>
+</span><span id="setup_logger-38"><a href="#setup_logger-38"><span class="linenos">38</span></a>        <span class="n">file_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">file_formatter</span><span class="p">)</span>
+</span><span id="setup_logger-39"><a href="#setup_logger-39"><span class="linenos">39</span></a>        <span class="n">stream_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s2">&quot;[</span><span class="si">%(levelname)s</span><span class="s2">] - </span><span class="si">%(message)s</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="setup_logger-40"><a href="#setup_logger-40"><span class="linenos">40</span></a>        <span class="n">stream_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">stream_formatter</span><span class="p">)</span>
+</span><span id="setup_logger-41"><a href="#setup_logger-41"><span class="linenos">41</span></a>
+</span><span id="setup_logger-42"><a href="#setup_logger-42"><span class="linenos">42</span></a>        <span class="c1"># Add the handlers to the logger</span>
+</span><span id="setup_logger-43"><a href="#setup_logger-43"><span class="linenos">43</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">file_handler</span><span class="p">)</span>
+</span><span id="setup_logger-44"><a href="#setup_logger-44"><span class="linenos">44</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">stream_handler</span><span class="p">)</span>
+</span><span id="setup_logger-45"><a href="#setup_logger-45"><span class="linenos">45</span></a>
+</span><span id="setup_logger-46"><a href="#setup_logger-46"><span class="linenos">46</span></a>    <span class="k">return</span> <span class="n">logger</span>
 </span></pre></div>
 
 
-            <div class="docstring"><p>Sets up logger as a singleton outputing to file and sysout syserr</p>
+            <div class="docstring"><p>Sets up acmc logger as a singleton outputing to file and sysout syserr.</p>
 </div>
 
 
@@ -182,18 +201,18 @@
 
     </div>
     <a class="headerlink" href="#set_log_level"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="set_log_level-40"><a href="#set_log_level-40"><span class="linenos">40</span></a><span class="k">def</span><span class="w"> </span><span class="nf">set_log_level</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
-</span><span id="set_log_level-41"><a href="#set_log_level-41"><span class="linenos">41</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Sets the log level for the acmc logger&quot;&quot;&quot;</span>
-</span><span id="set_log_level-42"><a href="#set_log_level-42"><span class="linenos">42</span></a>    <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">&quot;acmc_logger&quot;</span><span class="p">)</span>
-</span><span id="set_log_level-43"><a href="#set_log_level-43"><span class="linenos">43</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>  <span class="c1"># Set logger level</span>
-</span><span id="set_log_level-44"><a href="#set_log_level-44"><span class="linenos">44</span></a>
-</span><span id="set_log_level-45"><a href="#set_log_level-45"><span class="linenos">45</span></a>    <span class="c1"># Also update handlers to match the new level</span>
-</span><span id="set_log_level-46"><a href="#set_log_level-46"><span class="linenos">46</span></a>    <span class="k">for</span> <span class="n">handler</span> <span class="ow">in</span> <span class="n">logger</span><span class="o">.</span><span class="n">handlers</span><span class="p">:</span>
-</span><span id="set_log_level-47"><a href="#set_log_level-47"><span class="linenos">47</span></a>        <span class="n">handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="set_log_level-49"><a href="#set_log_level-49"><span class="linenos">49</span></a><span class="k">def</span><span class="w"> </span><span class="nf">set_log_level</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
+</span><span id="set_log_level-50"><a href="#set_log_level-50"><span class="linenos">50</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Sets the log level for the acmc logger.&quot;&quot;&quot;</span>
+</span><span id="set_log_level-51"><a href="#set_log_level-51"><span class="linenos">51</span></a>    <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">&quot;acmc_logger&quot;</span><span class="p">)</span>
+</span><span id="set_log_level-52"><a href="#set_log_level-52"><span class="linenos">52</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>
+</span><span id="set_log_level-53"><a href="#set_log_level-53"><span class="linenos">53</span></a>
+</span><span id="set_log_level-54"><a href="#set_log_level-54"><span class="linenos">54</span></a>    <span class="c1"># Also update handlers to match the new level</span>
+</span><span id="set_log_level-55"><a href="#set_log_level-55"><span class="linenos">55</span></a>    <span class="k">for</span> <span class="n">handler</span> <span class="ow">in</span> <span class="n">logger</span><span class="o">.</span><span class="n">handlers</span><span class="p">:</span>
+</span><span id="set_log_level-56"><a href="#set_log_level-56"><span class="linenos">56</span></a>        <span class="n">handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>
 </span></pre></div>
 
 
-            <div class="docstring"><p>Sets the log level for the acmc logger</p>
+            <div class="docstring"><p>Sets the log level for the acmc logger.</p>
 </div>
 
 
diff --git a/docs/api/acmc/omop.html b/docs/api/acmc/omop.html
index 879520eaf02437c47091e817a2655b29b0c9c63e..59f30a21103bfcb78847608bc59af300920f58b1 100644
--- a/docs/api/acmc/omop.html
+++ b/docs/api/acmc/omop.html
@@ -28,7 +28,7 @@
 
             <h2>Contents</h2>
             <ul>
-  <li><a href="#omop-module">OMOP Module</a></li>
+  <li><a href="#omop-module">omop module</a></li>
 </ul>
 
 
@@ -105,7 +105,7 @@
                     <h1 class="modulename">
 <a href="./../acmc.html">acmc</a><wbr>.omop    </h1>
 
-                        <div class="docstring"><h1 id="omop-module">OMOP Module</h1>
+                        <div class="docstring"><h1 id="omop-module">omop module</h1>
 
 <p>This module provides functionality to manage OMOP vocabularies.</p>
 </div>
@@ -115,7 +115,7 @@
                         <label class="view-source-button" for="mod-omop-view-source"><span>View Source</span></label>
 
                         <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos">  1</span></a><span class="sd">&quot;&quot;&quot;</span>
-</span><span id="L-2"><a href="#L-2"><span class="linenos">  2</span></a><span class="sd">OMOP Module</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos">  2</span></a><span class="sd">omop module</span>
 </span><span id="L-3"><a href="#L-3"><span class="linenos">  3</span></a><span class="sd">================</span>
 </span><span id="L-4"><a href="#L-4"><span class="linenos">  4</span></a><span class="sd">This module provides functionality to manage OMOP vocabularies.</span>
 </span><span id="L-5"><a href="#L-5"><span class="linenos">  5</span></a><span class="sd">&quot;&quot;&quot;</span>
@@ -178,276 +178,346 @@
 </span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a><span class="p">}</span>
 </span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a>
 </span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a>
-</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a><span class="c1"># Populate SQLite3 Database with default OMOP CONCEPTS</span>
-</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a><span class="k">def</span><span class="w"> </span><span class="nf">install</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
-</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Installs the OMOP release csv files in a file-based sql database&quot;&quot;&quot;</span>
-</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Installing OMOP from zip file: </span><span class="si">{</span><span class="n">omop_zip_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a>    <span class="n">omop_zip_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">)</span>
-</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a>
-</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a>    <span class="c1"># Check if the file exists and is a ZIP file</span>
-</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">omop_zip_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
-</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a>        <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> does not exist.&quot;</span>
-</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a>        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">is_zipfile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">):</span>
-</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a>        <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;Error: </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> is not a valid ZIP file.&quot;</span>
-</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a>        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a>
-</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a>    <span class="c1"># check codes directory exists and if not create it</span>
-</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
-</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a>        <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP directory &#39;</span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">&#39; created.&quot;</span><span class="p">)</span>
-</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a>    <span class="k">else</span><span class="p">:</span>
-</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a>        <span class="c1"># removing existing OMOP files</span>
-</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a>        <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
-</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a>        <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
-</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a>            <span class="n">file</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
-</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Deleted OMOP csv file: </span><span class="si">{</span><span class="n">file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a>
-</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a>    <span class="c1"># Extract ZIP contents</span>
-</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a>    <span class="k">with</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">zip_ref</span><span class="p">:</span>
-</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a>        <span class="n">zip_ref</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="p">)</span>
-</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Extracted OMOP zip file </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">/&quot;</span><span class="p">)</span>
-</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a>
-</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a>    <span class="c1"># connect to database, if it does not exist it will be created</span>
-</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">)</span>
-</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a>
-</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a>    <span class="c1"># Iterate through files in the folder</span>
-</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a>    <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
-</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a>    <span class="n">total_tables_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">csv_files</span><span class="p">)</span>
-</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a>    <span class="n">table_count</span> <span class="o">=</span> <span class="mi">1</span>
-</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a>    <span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
-</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a>        <span class="k">try</span><span class="p">:</span>
-</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
-</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a>                <span class="sa">f</span><span class="s2">&quot;Processing </span><span class="si">{</span><span class="n">table_count</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total_tables_count</span><span class="si">}</span><span class="s2"> tables: </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">&quot;</span>
-</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a>            <span class="p">)</span>
-</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a>            <span class="c1"># read the CSV file with the specified delimiter</span>
-</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a>            <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">low_memory</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a>
-</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a>            <span class="c1"># export Table to sqlite db</span>
-</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a>            <span class="n">df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;replace&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a>
-</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a>            <span class="c1"># add to the metadata</span>
-</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a>            <span class="nb">list</span><span class="p">(</span><span class="n">vocabularies</span><span class="p">[</span><span class="s2">&quot;tables&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">)</span>
-</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a>            <span class="n">table_count</span> <span class="o">=</span> <span class="n">table_count</span> <span class="o">+</span> <span class="mi">1</span>
-</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a>        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
-</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a>            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error reading file </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a>
-</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a>
-</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a>    <span class="c1"># write version file</span>
-</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a>    <span class="n">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
-</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a>
-</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP installation completed&quot;</span><span class="p">)</span>
-</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a>
-</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a>
-</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
-</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Writes the OMOP vocaburaries and version to a file&quot;&quot;&quot;</span>
-</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a>    <span class="n">vocabularies</span><span class="p">[</span><span class="s2">&quot;version&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">version</span>
-</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a>    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">VERSION_PATH</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
-</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a>        <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
-</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a>            <span class="n">vocabularies</span><span class="p">,</span>
-</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a>            <span class="n">file</span><span class="p">,</span>
-</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a>            <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
-</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a>            <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
-</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a>            <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
-</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a>            <span class="n">default_style</span><span class="o">=</span><span class="s1">&#39;&quot;&#39;</span><span class="p">,</span>
-</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a>        <span class="p">)</span>
+</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a><span class="k">def</span><span class="w"> </span><span class="nf">install</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;&quot;Installs the OMOP release csv files in a file-based sql database</span>
+</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a>
+</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a><span class="sd">    Args:</span>
+</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a><span class="sd">        omop_zip_file (str): vocabularies zip file distributed by OHDSI Athena</span>
+</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a><span class="sd">        version (str): version of the vocabularies distributed by OHDSI Athena</span>
+</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a>
+</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a><span class="sd">    Raises:</span>
+</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a><span class="sd">        ValueError: if the zip file does not exist</span>
+</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a><span class="sd">        ValueError: if the file is not a zip file</span>
+</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a><span class="sd">        Exception: if error reading omop csv files</span>
+</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Installing OMOP from zip file: </span><span class="si">{</span><span class="n">omop_zip_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a>    <span class="n">omop_zip_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">)</span>
+</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a>
+</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a>    <span class="c1"># Check if the file exists and is a ZIP file</span>
+</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">omop_zip_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a>        <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> does not exist.&quot;</span>
+</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a>        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a>    
+</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">is_zipfile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">):</span>
+</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a>        <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;Error: </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> is not a valid ZIP file.&quot;</span>
+</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a>        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a>
+</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a>    <span class="c1"># check codes directory exists and if not create it</span>
+</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a>        <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP directory &#39;</span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">&#39; created.&quot;</span><span class="p">)</span>
+</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a>    <span class="k">else</span><span class="p">:</span>
+</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a>        <span class="c1"># removing existing OMOP files</span>
+</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a>        <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
+</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a>        <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
+</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a>            <span class="n">file</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Deleted OMOP csv file: </span><span class="si">{</span><span class="n">file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a>
+</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a>    <span class="c1"># Extract ZIP contents</span>
+</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a>    <span class="k">with</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">zip_ref</span><span class="p">:</span>
+</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a>        <span class="n">zip_ref</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="p">)</span>
+</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Extracted OMOP zip file </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">/&quot;</span><span class="p">)</span>
+</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a>
+</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a>    <span class="c1"># connect to database, if it does not exist it will be created</span>
+</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">)</span>
+</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a>
+</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a>    <span class="c1"># Iterate through files in the folder</span>
+</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a>    <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
+</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a>    <span class="n">total_tables_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">csv_files</span><span class="p">)</span>
+</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a>    <span class="n">table_count</span> <span class="o">=</span> <span class="mi">1</span>
+</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a>    <span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
+</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a>        <span class="k">try</span><span class="p">:</span>
+</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a>                <span class="sa">f</span><span class="s2">&quot;Processing </span><span class="si">{</span><span class="n">table_count</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total_tables_count</span><span class="si">}</span><span class="s2"> tables: </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">&quot;</span>
+</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a>            <span class="p">)</span>
+</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a>            <span class="c1"># read the CSV file with the specified delimiter</span>
+</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a>            <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">low_memory</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a>
+</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a>            <span class="c1"># export Table to sqlite db</span>
+</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a>            <span class="n">df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;replace&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a>
+</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a>            <span class="c1"># add to the metadata</span>
+</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a>            <span class="nb">list</span><span class="p">(</span><span class="n">vocabularies</span><span class="p">[</span><span class="s2">&quot;tables&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">)</span>
+</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a>            <span class="n">table_count</span> <span class="o">=</span> <span class="n">table_count</span> <span class="o">+</span> <span class="mi">1</span>
+</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a>        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a>            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error reading file </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a>
+</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a>
+</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a>    <span class="c1"># write version file</span>
+</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a>    <span class="n">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
+</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a>
+</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP installation completed&quot;</span><span class="p">)</span>
+</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a>
+</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a>
+</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Writes the OMOP vocaburaries and version to a file</span>
 </span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a>
-</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a>
-</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a><span class="k">def</span><span class="w"> </span><span class="nf">clear</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
-</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Clears the OMOP sql database&quot;&quot;&quot;</span>
-</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Clearing OMOP data from database&quot;</span><span class="p">)</span>
-</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
-</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a>        <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error: OMOP DB file &#39;</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">&#39; does not exist.&quot;</span><span class="p">)</span>
-</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db_path</span><span class="p">)</span>
-</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a>    <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
-</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">&quot;SELECT name FROM sqlite_master WHERE type=&#39;table&#39;;&quot;</span><span class="p">)</span>
-</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a>
-</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a>    <span class="c1"># Fetch and print table names</span>
-</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a>    <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>
-</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Tables in database:&quot;</span><span class="p">,</span> <span class="p">[</span><span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">])</span>
+</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a><span class="sd">    Args:</span>
+</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a><span class="sd">        version (str): version of the vocabularies distributed by OHDSI Athena</span>
+</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a>    <span class="n">vocabularies</span><span class="p">[</span><span class="s2">&quot;version&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">version</span>
+</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a>    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">VERSION_PATH</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a>        <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a>            <span class="n">vocabularies</span><span class="p">,</span>
+</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a>            <span class="n">file</span><span class="p">,</span>
+</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a>            <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a>            <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a>            <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a>            <span class="n">default_style</span><span class="o">=</span><span class="s1">&#39;&quot;&#39;</span><span class="p">,</span>
+</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a>        <span class="p">)</span>
 </span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a>
-</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a>    <span class="c1"># cur.execute(&quot;DROP TABLE CONCEPT_SET;&quot;)</span>
-</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a>    <span class="c1"># cur.execute(&quot;DROP TABLE CONCEPT_SET_ITEM;&quot;)</span>
-</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a>
-</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP database cleared&quot;</span><span class="p">)</span>
-</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a>
+</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a>
+</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a><span class="k">def</span><span class="w"> </span><span class="nf">clear</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Clears the OMOP sql database</span>
+</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a>
+</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a><span class="sd">    Args:</span>
+</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a><span class="sd">        db_path (Path): the path to the omop sqllite database</span>
 </span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a>
-</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a><span class="k">def</span><span class="w"> </span><span class="nf">delete</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
-</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Deletes the OMOP sql database&quot;&quot;&quot;</span>
-</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Deleting OMOP database&quot;</span><span class="p">)</span>
-</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
-</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a>        <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error: OMOP DB file &#39;</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">&#39; does not exist.&quot;</span><span class="p">)</span>
-</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a>
-</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a>    <span class="n">db_path</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
-</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP database deleted&quot;</span><span class="p">)</span>
-</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a>
+</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a><span class="sd">    Raises:</span>
+</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a><span class="sd">        FileNotFoundError: if the omop sqllite database does not exist</span>
+</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Clearing OMOP data from database&quot;</span><span class="p">)</span>
+</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a>        <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error: OMOP DB file &#39;</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">&#39; does not exist.&quot;</span><span class="p">)</span>
+</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db_path</span><span class="p">)</span>
+</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a>    <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">&quot;SELECT name FROM sqlite_master WHERE type=&#39;table&#39;;&quot;</span><span class="p">)</span>
 </span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a>
-</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a><span class="k">def</span><span class="w"> </span><span class="nf">table_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">table_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a>    <span class="c1"># Query to check if the table exists</span>
-</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a><span class="sd">		SELECT name</span>
-</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a><span class="sd">		FROM sqlite_master</span>
-</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a><span class="sd">		WHERE type=&#39;table&#39; AND name=?</span>
-</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a><span class="sd">		&quot;&quot;&quot;</span><span class="p">,</span>
-</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a>        <span class="p">(</span><span class="n">table_name</span><span class="p">,),</span>
-</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a>    <span class="p">)</span>
+</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a>    <span class="c1"># Fetch and print table names</span>
+</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a>    <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>
+</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Tables in database:&quot;</span><span class="p">,</span> <span class="p">[</span><span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">])</span>
+</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a>
+</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a>    <span class="c1"># cur.execute(&quot;DROP TABLE CONCEPT_SET;&quot;)</span>
+</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a>    <span class="c1"># cur.execute(&quot;DROP TABLE CONCEPT_SET_ITEM;&quot;)</span>
+</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a>
+</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP database cleared&quot;</span><span class="p">)</span>
+</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a>
 </span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a>
-</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a>    <span class="c1"># Fetch the result</span>
-</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a>    <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a><span class="k">def</span><span class="w"> </span><span class="nf">delete</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Deletes the OMOP sql database</span>
 </span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a>
-</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a>    <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
-</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a>
+</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a><span class="sd">    Args:</span>
+</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a><span class="sd">        db_path (Path): the path to the omop sqllite database</span>
 </span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a>
-</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a><span class="k">def</span><span class="w"> </span><span class="nf">vocab_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">vocab_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a>    <span class="c1"># Query to check if the table exists</span>
-</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a><span class="sd">		SELECT vocabulary_id </span>
-</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a><span class="sd">		FROM VOCABULARY</span>
-</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a><span class="sd">		WHERE vocabulary_id=?</span>
-</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a><span class="sd">		&quot;&quot;&quot;</span><span class="p">,</span>
-</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a>        <span class="p">(</span><span class="n">vocab_id</span><span class="p">,),</span>
-</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a>    <span class="p">)</span>
+</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a><span class="sd">    Raises:</span>
+</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a><span class="sd">        FileNotFoundError: if the omop sqllite database does not exist</span>
+</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a>    
+</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Deleting OMOP database&quot;</span><span class="p">)</span>
+</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a>        <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error: OMOP DB file &#39;</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">&#39; does not exist.&quot;</span><span class="p">)</span>
+</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a>
+</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a>    <span class="n">db_path</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP database deleted&quot;</span><span class="p">)</span>
 </span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a>
-</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a>    <span class="c1"># Fetch the result</span>
-</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a>    <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
-</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a>
-</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a>    <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
-</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a>
-</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a>
-</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a><span class="k">def</span><span class="w"> </span><span class="nf">concept_set_exist</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">concept_set_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a>    <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;SELECT EXISTS (SELECT 1 FROM CONCEPT_SET WHERE concept_set_name = ?)&quot;</span>
-</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">concept_set_name</span><span class="p">,))</span>
-</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a>
-</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a>    <span class="c1"># 1 if exists, 0 otherwise</span>
-</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a>    <span class="k">return</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span>
-</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a>
-</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a>
-</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a><span class="k">def</span><span class="w"> </span><span class="nf">export</span><span class="p">(</span><span class="n">map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">export_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">omop_metadata</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Path</span><span class="p">:</span>
-</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;exporting with metadata </span><span class="si">{</span><span class="n">omop_metadata</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a>
-</span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a>    <span class="c1"># copy the baseline omop database</span>
-</span><span id="L-219"><a href="#L-219"><span class="linenos">219</span></a>    <span class="n">export_db_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">EXPORT_FILE</span>
-</span><span id="L-220"><a href="#L-220"><span class="linenos">220</span></a>    <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">,</span> <span class="n">export_db_path</span><span class="p">)</span>
+</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a>
+</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a><span class="k">def</span><span class="w"> </span><span class="nf">table_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">table_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Query to check if the table exists</span>
+</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a>
+</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a><span class="sd">    Args:</span>
+</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a><span class="sd">        cursor (sqlite3.Cursor): a sqllite database cursor</span>
+</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a><span class="sd">        table_name (str): the table name to check</span>
+</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a>
+</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a><span class="sd">    Returns:</span>
+</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a><span class="sd">        bool: true if table exists</span>
+</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a><span class="sd">    &quot;&quot;&quot;</span>    
+</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a>        
+</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a><span class="sd">		SELECT name</span>
+</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a><span class="sd">		FROM sqlite_master</span>
+</span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a><span class="sd">		WHERE type=&#39;table&#39; AND name=?</span>
+</span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a><span class="sd">		&quot;&quot;&quot;</span><span class="p">,</span>
+</span><span id="L-219"><a href="#L-219"><span class="linenos">219</span></a>        <span class="p">(</span><span class="n">table_name</span><span class="p">,),</span>
+</span><span id="L-220"><a href="#L-220"><span class="linenos">220</span></a>    <span class="p">)</span>
 </span><span id="L-221"><a href="#L-221"><span class="linenos">221</span></a>
-</span><span id="L-222"><a href="#L-222"><span class="linenos">222</span></a>    <span class="c1"># connect to db</span>
-</span><span id="L-223"><a href="#L-223"><span class="linenos">223</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">export_db_path</span><span class="p">)</span>
-</span><span id="L-224"><a href="#L-224"><span class="linenos">224</span></a>    <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
-</span><span id="L-225"><a href="#L-225"><span class="linenos">225</span></a>
-</span><span id="L-226"><a href="#L-226"><span class="linenos">226</span></a>    <span class="c1"># Create VOCABULARY</span>
-</span><span id="L-227"><a href="#L-227"><span class="linenos">227</span></a>    <span class="n">df_test</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
-</span><span id="L-228"><a href="#L-228"><span class="linenos">228</span></a>        <span class="p">[</span>
-</span><span id="L-229"><a href="#L-229"><span class="linenos">229</span></a>            <span class="p">{</span>
-</span><span id="L-230"><a href="#L-230"><span class="linenos">230</span></a>                <span class="s2">&quot;vocabulary_id&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_id&quot;</span><span class="p">],</span>
-</span><span id="L-231"><a href="#L-231"><span class="linenos">231</span></a>                <span class="s2">&quot;vocabulary_name&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_name&quot;</span><span class="p">],</span>
-</span><span id="L-232"><a href="#L-232"><span class="linenos">232</span></a>                <span class="s2">&quot;vocabulary_reference&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_reference&quot;</span><span class="p">],</span>
-</span><span id="L-233"><a href="#L-233"><span class="linenos">233</span></a>                <span class="s2">&quot;vocabulary_version&quot;</span><span class="p">:</span> <span class="n">version</span><span class="p">,</span>
-</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a>                <span class="c1"># &quot;vocabulary_concept_id&quot;: 0,</span>
-</span><span id="L-235"><a href="#L-235"><span class="linenos">235</span></a>            <span class="p">}</span>
-</span><span id="L-236"><a href="#L-236"><span class="linenos">236</span></a>        <span class="p">]</span>
-</span><span id="L-237"><a href="#L-237"><span class="linenos">237</span></a>    <span class="p">)</span>
-</span><span id="L-238"><a href="#L-238"><span class="linenos">238</span></a>    <span class="n">df_test</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">&quot;VOCABULARY&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;append&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-</span><span id="L-239"><a href="#L-239"><span class="linenos">239</span></a>
-</span><span id="L-240"><a href="#L-240"><span class="linenos">240</span></a>    <span class="c1"># Create CONCEPT_SET</span>
-</span><span id="L-241"><a href="#L-241"><span class="linenos">241</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="L-242"><a href="#L-242"><span class="linenos">242</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-</span><span id="L-243"><a href="#L-243"><span class="linenos">243</span></a><span class="sd">	CREATE TABLE CONCEPT_SET (</span>
-</span><span id="L-244"><a href="#L-244"><span class="linenos">244</span></a><span class="sd">		concept_set_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each concept set</span>
-</span><span id="L-245"><a href="#L-245"><span class="linenos">245</span></a><span class="sd">		atlas_id INTEGER,                                -- Unique identifier generated by ATLAS</span>
-</span><span id="L-246"><a href="#L-246"><span class="linenos">246</span></a><span class="sd">		concept_set_name TEXT,                           -- Optional name for the concept set</span>
-</span><span id="L-247"><a href="#L-247"><span class="linenos">247</span></a><span class="sd">		concept_set_description TEXT,                    -- Optional description for the concept set</span>
-</span><span id="L-248"><a href="#L-248"><span class="linenos">248</span></a><span class="sd">		vocabulary_id TEXT NOT NULL,                     -- Foreign key to VOCABULARY table</span>
-</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a><span class="sd">		FOREIGN KEY (vocabulary_id) REFERENCES VOCABULARY(vocabulary_id)</span>
-</span><span id="L-250"><a href="#L-250"><span class="linenos">250</span></a><span class="sd">	);&quot;&quot;&quot;</span>
-</span><span id="L-251"><a href="#L-251"><span class="linenos">251</span></a>    <span class="p">)</span>
+</span><span id="L-222"><a href="#L-222"><span class="linenos">222</span></a>    <span class="c1"># Fetch the result</span>
+</span><span id="L-223"><a href="#L-223"><span class="linenos">223</span></a>    <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+</span><span id="L-224"><a href="#L-224"><span class="linenos">224</span></a>
+</span><span id="L-225"><a href="#L-225"><span class="linenos">225</span></a>    <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+</span><span id="L-226"><a href="#L-226"><span class="linenos">226</span></a>
+</span><span id="L-227"><a href="#L-227"><span class="linenos">227</span></a>
+</span><span id="L-228"><a href="#L-228"><span class="linenos">228</span></a><span class="k">def</span><span class="w"> </span><span class="nf">vocab_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">vocab_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="L-229"><a href="#L-229"><span class="linenos">229</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Query to check if the vocabulary exists</span>
+</span><span id="L-230"><a href="#L-230"><span class="linenos">230</span></a>
+</span><span id="L-231"><a href="#L-231"><span class="linenos">231</span></a><span class="sd">    Args:</span>
+</span><span id="L-232"><a href="#L-232"><span class="linenos">232</span></a><span class="sd">        cursor (sqlite3.Cursor): a sqllite database cursor</span>
+</span><span id="L-233"><a href="#L-233"><span class="linenos">233</span></a><span class="sd">        vocab_id (str): the vocabulary id to check</span>
+</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a>
+</span><span id="L-235"><a href="#L-235"><span class="linenos">235</span></a><span class="sd">    Returns:</span>
+</span><span id="L-236"><a href="#L-236"><span class="linenos">236</span></a><span class="sd">        bool: true if vocabulary id exists</span>
+</span><span id="L-237"><a href="#L-237"><span class="linenos">237</span></a><span class="sd">    &quot;&quot;&quot;</span>    
+</span><span id="L-238"><a href="#L-238"><span class="linenos">238</span></a>    
+</span><span id="L-239"><a href="#L-239"><span class="linenos">239</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-240"><a href="#L-240"><span class="linenos">240</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="L-241"><a href="#L-241"><span class="linenos">241</span></a><span class="sd">		SELECT vocabulary_id </span>
+</span><span id="L-242"><a href="#L-242"><span class="linenos">242</span></a><span class="sd">		FROM VOCABULARY</span>
+</span><span id="L-243"><a href="#L-243"><span class="linenos">243</span></a><span class="sd">		WHERE vocabulary_id=?</span>
+</span><span id="L-244"><a href="#L-244"><span class="linenos">244</span></a><span class="sd">		&quot;&quot;&quot;</span><span class="p">,</span>
+</span><span id="L-245"><a href="#L-245"><span class="linenos">245</span></a>        <span class="p">(</span><span class="n">vocab_id</span><span class="p">,),</span>
+</span><span id="L-246"><a href="#L-246"><span class="linenos">246</span></a>    <span class="p">)</span>
+</span><span id="L-247"><a href="#L-247"><span class="linenos">247</span></a>
+</span><span id="L-248"><a href="#L-248"><span class="linenos">248</span></a>    <span class="c1"># Fetch the result</span>
+</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a>    <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+</span><span id="L-250"><a href="#L-250"><span class="linenos">250</span></a>
+</span><span id="L-251"><a href="#L-251"><span class="linenos">251</span></a>    <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
 </span><span id="L-252"><a href="#L-252"><span class="linenos">252</span></a>
-</span><span id="L-253"><a href="#L-253"><span class="linenos">253</span></a>    <span class="c1"># Create CONCEPT_SET_ITEM</span>
-</span><span id="L-254"><a href="#L-254"><span class="linenos">254</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="L-255"><a href="#L-255"><span class="linenos">255</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-</span><span id="L-256"><a href="#L-256"><span class="linenos">256</span></a><span class="sd">	CREATE TABLE CONCEPT_SET_ITEM (</span>
-</span><span id="L-257"><a href="#L-257"><span class="linenos">257</span></a><span class="sd">		concept_set_item_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each mapping</span>
-</span><span id="L-258"><a href="#L-258"><span class="linenos">258</span></a><span class="sd">		concept_set_id INTEGER NOT NULL,                      -- Foreign key to CONCEPT_SET table</span>
-</span><span id="L-259"><a href="#L-259"><span class="linenos">259</span></a><span class="sd">		concept_id INTEGER NOT NULL,                          -- Foreign key to CONCEPT table</span>
-</span><span id="L-260"><a href="#L-260"><span class="linenos">260</span></a><span class="sd">		FOREIGN KEY (concept_set_id) REFERENCES CONCEPT_SET(concept_set_id),</span>
-</span><span id="L-261"><a href="#L-261"><span class="linenos">261</span></a><span class="sd">		FOREIGN KEY (concept_id) REFERENCES CONCEPT(concept_id)</span>
-</span><span id="L-262"><a href="#L-262"><span class="linenos">262</span></a><span class="sd">	);&quot;&quot;&quot;</span>
-</span><span id="L-263"><a href="#L-263"><span class="linenos">263</span></a>    <span class="p">)</span>
-</span><span id="L-264"><a href="#L-264"><span class="linenos">264</span></a>
-</span><span id="L-265"><a href="#L-265"><span class="linenos">265</span></a>    <span class="c1"># read map files</span>
-</span><span id="L-266"><a href="#L-266"><span class="linenos">266</span></a>    <span class="n">map_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
-</span><span id="L-267"><a href="#L-267"><span class="linenos">267</span></a>    <span class="n">total</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">map_files</span><span class="p">)</span>
-</span><span id="L-268"><a href="#L-268"><span class="linenos">268</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Exporting </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2"> map files&quot;</span><span class="p">)</span>
-</span><span id="L-269"><a href="#L-269"><span class="linenos">269</span></a>    <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">map_file</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">map_files</span><span class="p">):</span>
-</span><span id="L-270"><a href="#L-270"><span class="linenos">270</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Processing </span><span class="si">{</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">map_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="L-271"><a href="#L-271"><span class="linenos">271</span></a>        <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">map_file</span><span class="p">)</span>
-</span><span id="L-272"><a href="#L-272"><span class="linenos">272</span></a>
-</span><span id="L-273"><a href="#L-273"><span class="linenos">273</span></a>        <span class="k">for</span> <span class="n">concept_set_name</span><span class="p">,</span> <span class="n">grp</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">&quot;CONCEPT_SET&quot;</span><span class="p">):</span>
-</span><span id="L-274"><a href="#L-274"><span class="linenos">274</span></a>            <span class="c1"># create Concept_Set</span>
-</span><span id="L-275"><a href="#L-275"><span class="linenos">275</span></a>            <span class="k">if</span> <span class="ow">not</span> <span class="n">concept_set_exist</span><span class="p">(</span><span class="n">cur</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">concept_set_name</span><span class="p">)):</span>
-</span><span id="L-276"><a href="#L-276"><span class="linenos">276</span></a>                <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="L-277"><a href="#L-277"><span class="linenos">277</span></a>                    <span class="sa">f</span><span class="s2">&quot;INSERT INTO CONCEPT_SET (concept_set_name, vocabulary_id) VALUES (&#39;</span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2">&#39;, &#39;</span><span class="si">{</span><span class="n">omop_metadata</span><span class="p">[</span><span class="s1">&#39;vocabulary_id&#39;</span><span class="p">]</span><span class="si">}</span><span class="s2">&#39;);&quot;</span>
-</span><span id="L-278"><a href="#L-278"><span class="linenos">278</span></a>                <span class="p">)</span>
-</span><span id="L-279"><a href="#L-279"><span class="linenos">279</span></a>            <span class="k">else</span><span class="p">:</span>
-</span><span id="L-280"><a href="#L-280"><span class="linenos">280</span></a>                <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Concept_set </span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2"> already exists&quot;</span><span class="p">)</span>
-</span><span id="L-281"><a href="#L-281"><span class="linenos">281</span></a>                <span class="c1"># TODO: ask to remove old concept_set?</span>
-</span><span id="L-282"><a href="#L-282"><span class="linenos">282</span></a>
-</span><span id="L-283"><a href="#L-283"><span class="linenos">283</span></a>            <span class="c1"># get Concept_set_Id</span>
-</span><span id="L-284"><a href="#L-284"><span class="linenos">284</span></a>            <span class="n">query</span> <span class="o">=</span> <span class="s2">&quot;SELECT concept_set_id FROM CONCEPT_SET WHERE concept_set_name = ? AND vocabulary_id = ?;&quot;</span>
-</span><span id="L-285"><a href="#L-285"><span class="linenos">285</span></a>            <span class="n">target_code_type</span> <span class="o">=</span> <span class="n">map_file</span><span class="o">.</span><span class="n">stem</span>
-</span><span id="L-286"><a href="#L-286"><span class="linenos">286</span></a>            <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="L-287"><a href="#L-287"><span class="linenos">287</span></a>                <span class="n">query</span><span class="p">,</span>
-</span><span id="L-288"><a href="#L-288"><span class="linenos">288</span></a>                <span class="p">(</span>
-</span><span id="L-289"><a href="#L-289"><span class="linenos">289</span></a>                    <span class="n">concept_set_name</span><span class="p">,</span>
-</span><span id="L-290"><a href="#L-290"><span class="linenos">290</span></a>                    <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_id&quot;</span><span class="p">],</span>
-</span><span id="L-291"><a href="#L-291"><span class="linenos">291</span></a>                <span class="p">),</span>
-</span><span id="L-292"><a href="#L-292"><span class="linenos">292</span></a>            <span class="p">)</span>
-</span><span id="L-293"><a href="#L-293"><span class="linenos">293</span></a>            <span class="c1"># FAILS HERE WITH NONE REUR</span>
-</span><span id="L-294"><a href="#L-294"><span class="linenos">294</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="L-295"><a href="#L-295"><span class="linenos">295</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;omop code type </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="L-296"><a href="#L-296"><span class="linenos">296</span></a>            <span class="n">concept_set_id</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
-</span><span id="L-297"><a href="#L-297"><span class="linenos">297</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;concept set id </span><span class="si">{</span><span class="n">concept_set_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="L-298"><a href="#L-298"><span class="linenos">298</span></a>
-</span><span id="L-299"><a href="#L-299"><span class="linenos">299</span></a>            <span class="c1"># get corresponing Concept_id (OMOP) for each Concept_code (e.g. SNOMED)</span>
-</span><span id="L-300"><a href="#L-300"><span class="linenos">300</span></a>            <span class="n">concept_codes</span> <span class="o">=</span> <span class="s2">&quot;&#39;&quot;</span> <span class="o">+</span> <span class="s2">&quot;&#39;, &#39;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">grp</span><span class="p">[</span><span class="s2">&quot;CONCEPT&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)))</span> <span class="o">+</span> <span class="s2">&quot;&#39;&quot;</span>
-</span><span id="L-301"><a href="#L-301"><span class="linenos">301</span></a>            <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;SELECT concept_id FROM CONCEPT WHERE vocabulary_id = ? AND concept_code IN (</span><span class="si">{</span><span class="n">concept_codes</span><span class="si">}</span><span class="s2">);&quot;</span>
-</span><span id="L-302"><a href="#L-302"><span class="linenos">302</span></a>            <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">],))</span>
-</span><span id="L-303"><a href="#L-303"><span class="linenos">303</span></a>            <span class="n">df_out</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">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">(),</span> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;concept_id&quot;</span><span class="p">])</span>
-</span><span id="L-304"><a href="#L-304"><span class="linenos">304</span></a>
-</span><span id="L-305"><a href="#L-305"><span class="linenos">305</span></a>            <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">grp</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">df_out</span><span class="p">):</span>
-</span><span id="L-306"><a href="#L-306"><span class="linenos">306</span></a>                <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
-</span><span id="L-307"><a href="#L-307"><span class="linenos">307</span></a>                    <span class="sa">f</span><span class="s2">&quot;ERROR: Some </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2"> Codes do not exist in OMOP Database&quot;</span>
-</span><span id="L-308"><a href="#L-308"><span class="linenos">308</span></a>                <span class="p">)</span>
+</span><span id="L-253"><a href="#L-253"><span class="linenos">253</span></a>
+</span><span id="L-254"><a href="#L-254"><span class="linenos">254</span></a><span class="k">def</span><span class="w"> </span><span class="nf">concept_set_exist</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">concept_set_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="L-255"><a href="#L-255"><span class="linenos">255</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Query to check if the concept set exists</span>
+</span><span id="L-256"><a href="#L-256"><span class="linenos">256</span></a>
+</span><span id="L-257"><a href="#L-257"><span class="linenos">257</span></a><span class="sd">    Args:</span>
+</span><span id="L-258"><a href="#L-258"><span class="linenos">258</span></a><span class="sd">        cursor (sqlite3.Cursor): a sqllite database cursor</span>
+</span><span id="L-259"><a href="#L-259"><span class="linenos">259</span></a><span class="sd">        concept_set_name (str): the concept set name to check</span>
+</span><span id="L-260"><a href="#L-260"><span class="linenos">260</span></a>
+</span><span id="L-261"><a href="#L-261"><span class="linenos">261</span></a><span class="sd">    Returns:</span>
+</span><span id="L-262"><a href="#L-262"><span class="linenos">262</span></a><span class="sd">        bool: true if concept set exists</span>
+</span><span id="L-263"><a href="#L-263"><span class="linenos">263</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="L-264"><a href="#L-264"><span class="linenos">264</span></a>    
+</span><span id="L-265"><a href="#L-265"><span class="linenos">265</span></a>    <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;SELECT EXISTS (SELECT 1 FROM CONCEPT_SET WHERE concept_set_name = ?)&quot;</span>
+</span><span id="L-266"><a href="#L-266"><span class="linenos">266</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">concept_set_name</span><span class="p">,))</span>
+</span><span id="L-267"><a href="#L-267"><span class="linenos">267</span></a>
+</span><span id="L-268"><a href="#L-268"><span class="linenos">268</span></a>    <span class="c1"># 1 if exists, 0 otherwise</span>
+</span><span id="L-269"><a href="#L-269"><span class="linenos">269</span></a>    <span class="k">return</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span>
+</span><span id="L-270"><a href="#L-270"><span class="linenos">270</span></a>
+</span><span id="L-271"><a href="#L-271"><span class="linenos">271</span></a>
+</span><span id="L-272"><a href="#L-272"><span class="linenos">272</span></a><span class="k">def</span><span class="w"> </span><span class="nf">export</span><span class="p">(</span><span class="n">map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">export_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">omop_metadata</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Path</span><span class="p">:</span>
+</span><span id="L-273"><a href="#L-273"><span class="linenos">273</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Export concept sets to omop database in csv format</span>
+</span><span id="L-274"><a href="#L-274"><span class="linenos">274</span></a>
+</span><span id="L-275"><a href="#L-275"><span class="linenos">275</span></a><span class="sd">    Args:</span>
+</span><span id="L-276"><a href="#L-276"><span class="linenos">276</span></a><span class="sd">        map_path (Path): path to the acmc map directory containing concept sets in csv format</span>
+</span><span id="L-277"><a href="#L-277"><span class="linenos">277</span></a><span class="sd">        export_path (Path): path to the directory where the omop database csv files are to be written</span>
+</span><span id="L-278"><a href="#L-278"><span class="linenos">278</span></a><span class="sd">        version (str): phenotype version for omop vocabulary version</span>
+</span><span id="L-279"><a href="#L-279"><span class="linenos">279</span></a><span class="sd">        omop_metadata (dict): phenotype omop metadata for omop vocabulary metadata </span>
+</span><span id="L-280"><a href="#L-280"><span class="linenos">280</span></a><span class="sd">                </span>
+</span><span id="L-281"><a href="#L-281"><span class="linenos">281</span></a><span class="sd">    Returns:</span>
+</span><span id="L-282"><a href="#L-282"><span class="linenos">282</span></a><span class="sd">        Path: path to the exported sqllite database</span>
+</span><span id="L-283"><a href="#L-283"><span class="linenos">283</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="L-284"><a href="#L-284"><span class="linenos">284</span></a>    
+</span><span id="L-285"><a href="#L-285"><span class="linenos">285</span></a>    
+</span><span id="L-286"><a href="#L-286"><span class="linenos">286</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;exporting with metadata </span><span class="si">{</span><span class="n">omop_metadata</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="L-287"><a href="#L-287"><span class="linenos">287</span></a>
+</span><span id="L-288"><a href="#L-288"><span class="linenos">288</span></a>    <span class="c1"># copy the baseline omop database</span>
+</span><span id="L-289"><a href="#L-289"><span class="linenos">289</span></a>    <span class="n">export_db_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">EXPORT_FILE</span>
+</span><span id="L-290"><a href="#L-290"><span class="linenos">290</span></a>    <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">,</span> <span class="n">export_db_path</span><span class="p">)</span>
+</span><span id="L-291"><a href="#L-291"><span class="linenos">291</span></a>
+</span><span id="L-292"><a href="#L-292"><span class="linenos">292</span></a>    <span class="c1"># connect to db</span>
+</span><span id="L-293"><a href="#L-293"><span class="linenos">293</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">export_db_path</span><span class="p">)</span>
+</span><span id="L-294"><a href="#L-294"><span class="linenos">294</span></a>    <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="L-295"><a href="#L-295"><span class="linenos">295</span></a>
+</span><span id="L-296"><a href="#L-296"><span class="linenos">296</span></a>    <span class="c1"># Create VOCABULARY</span>
+</span><span id="L-297"><a href="#L-297"><span class="linenos">297</span></a>    <span class="n">df_test</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="L-298"><a href="#L-298"><span class="linenos">298</span></a>        <span class="p">[</span>
+</span><span id="L-299"><a href="#L-299"><span class="linenos">299</span></a>            <span class="p">{</span>
+</span><span id="L-300"><a href="#L-300"><span class="linenos">300</span></a>                <span class="s2">&quot;vocabulary_id&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_id&quot;</span><span class="p">],</span>
+</span><span id="L-301"><a href="#L-301"><span class="linenos">301</span></a>                <span class="s2">&quot;vocabulary_name&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_name&quot;</span><span class="p">],</span>
+</span><span id="L-302"><a href="#L-302"><span class="linenos">302</span></a>                <span class="s2">&quot;vocabulary_reference&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_reference&quot;</span><span class="p">],</span>
+</span><span id="L-303"><a href="#L-303"><span class="linenos">303</span></a>                <span class="s2">&quot;vocabulary_version&quot;</span><span class="p">:</span> <span class="n">version</span><span class="p">,</span>
+</span><span id="L-304"><a href="#L-304"><span class="linenos">304</span></a>                <span class="c1"># &quot;vocabulary_concept_id&quot;: 0,</span>
+</span><span id="L-305"><a href="#L-305"><span class="linenos">305</span></a>            <span class="p">}</span>
+</span><span id="L-306"><a href="#L-306"><span class="linenos">306</span></a>        <span class="p">]</span>
+</span><span id="L-307"><a href="#L-307"><span class="linenos">307</span></a>    <span class="p">)</span>
+</span><span id="L-308"><a href="#L-308"><span class="linenos">308</span></a>    <span class="n">df_test</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">&quot;VOCABULARY&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;append&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
 </span><span id="L-309"><a href="#L-309"><span class="linenos">309</span></a>
-</span><span id="L-310"><a href="#L-310"><span class="linenos">310</span></a>            <span class="c1"># Create Concept_set_item</span>
-</span><span id="L-311"><a href="#L-311"><span class="linenos">311</span></a>            <span class="n">df_out</span><span class="p">[</span><span class="s2">&quot;concept_set_id&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">concept_set_id</span>
-</span><span id="L-312"><a href="#L-312"><span class="linenos">312</span></a>            <span class="n">df_out</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">&quot;CONCEPT_SET_ITEM&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;append&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-</span><span id="L-313"><a href="#L-313"><span class="linenos">313</span></a>
-</span><span id="L-314"><a href="#L-314"><span class="linenos">314</span></a>    <span class="c1"># Output all tables to CSV</span>
-</span><span id="L-315"><a href="#L-315"><span class="linenos">315</span></a>    <span class="c1"># Get the list of all tables</span>
-</span><span id="L-316"><a href="#L-316"><span class="linenos">316</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">&quot;SELECT name FROM sqlite_master WHERE type=&#39;table&#39;;&quot;</span><span class="p">)</span>
-</span><span id="L-317"><a href="#L-317"><span class="linenos">317</span></a>    <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>  <span class="c1"># List of tables</span>
-</span><span id="L-318"><a href="#L-318"><span class="linenos">318</span></a>
-</span><span id="L-319"><a href="#L-319"><span class="linenos">319</span></a>    <span class="c1"># Export each table to a separate CSV file</span>
-</span><span id="L-320"><a href="#L-320"><span class="linenos">320</span></a>    <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">:</span>
-</span><span id="L-321"><a href="#L-321"><span class="linenos">321</span></a>        <span class="n">table_name</span> <span class="o">=</span> <span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-</span><span id="L-322"><a href="#L-322"><span class="linenos">322</span></a>        <span class="c1"># ignore SQLite&#39;s internal system table</span>
-</span><span id="L-323"><a href="#L-323"><span class="linenos">323</span></a>        <span class="k">if</span> <span class="n">table_name</span> <span class="o">!=</span> <span class="s2">&quot;sqlite_sequence&quot;</span><span class="p">:</span>
-</span><span id="L-324"><a href="#L-324"><span class="linenos">324</span></a>            <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql_query</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;SELECT * FROM </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
-</span><span id="L-325"><a href="#L-325"><span class="linenos">325</span></a>            <span class="n">output_file</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv&quot;</span>
-</span><span id="L-326"><a href="#L-326"><span class="linenos">326</span></a>            <span class="n">output_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">output_file</span>
-</span><span id="L-327"><a href="#L-327"><span class="linenos">327</span></a>            <span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>  <span class="c1"># Save as CSV</span>
-</span><span id="L-328"><a href="#L-328"><span class="linenos">328</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Exported </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">)</span>
-</span><span id="L-329"><a href="#L-329"><span class="linenos">329</span></a>
-</span><span id="L-330"><a href="#L-330"><span class="linenos">330</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</span><span id="L-331"><a href="#L-331"><span class="linenos">331</span></a>
-</span><span id="L-332"><a href="#L-332"><span class="linenos">332</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Created export db successfully&quot;</span><span class="p">)</span>
-</span><span id="L-333"><a href="#L-333"><span class="linenos">333</span></a>
-</span><span id="L-334"><a href="#L-334"><span class="linenos">334</span></a>    <span class="k">return</span> <span class="n">export_db_path</span>
+</span><span id="L-310"><a href="#L-310"><span class="linenos">310</span></a>    <span class="c1"># Create CONCEPT_SET</span>
+</span><span id="L-311"><a href="#L-311"><span class="linenos">311</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-312"><a href="#L-312"><span class="linenos">312</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="L-313"><a href="#L-313"><span class="linenos">313</span></a><span class="sd">	CREATE TABLE CONCEPT_SET (</span>
+</span><span id="L-314"><a href="#L-314"><span class="linenos">314</span></a><span class="sd">		concept_set_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each concept set</span>
+</span><span id="L-315"><a href="#L-315"><span class="linenos">315</span></a><span class="sd">		atlas_id INTEGER,                                -- Unique identifier generated by ATLAS</span>
+</span><span id="L-316"><a href="#L-316"><span class="linenos">316</span></a><span class="sd">		concept_set_name TEXT,                           -- Optional name for the concept set</span>
+</span><span id="L-317"><a href="#L-317"><span class="linenos">317</span></a><span class="sd">		concept_set_description TEXT,                    -- Optional description for the concept set</span>
+</span><span id="L-318"><a href="#L-318"><span class="linenos">318</span></a><span class="sd">		vocabulary_id TEXT NOT NULL,                     -- Foreign key to VOCABULARY table</span>
+</span><span id="L-319"><a href="#L-319"><span class="linenos">319</span></a><span class="sd">		FOREIGN KEY (vocabulary_id) REFERENCES VOCABULARY(vocabulary_id)</span>
+</span><span id="L-320"><a href="#L-320"><span class="linenos">320</span></a><span class="sd">	);&quot;&quot;&quot;</span>
+</span><span id="L-321"><a href="#L-321"><span class="linenos">321</span></a>    <span class="p">)</span>
+</span><span id="L-322"><a href="#L-322"><span class="linenos">322</span></a>
+</span><span id="L-323"><a href="#L-323"><span class="linenos">323</span></a>    <span class="c1"># Create CONCEPT_SET_ITEM</span>
+</span><span id="L-324"><a href="#L-324"><span class="linenos">324</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-325"><a href="#L-325"><span class="linenos">325</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="L-326"><a href="#L-326"><span class="linenos">326</span></a><span class="sd">	CREATE TABLE CONCEPT_SET_ITEM (</span>
+</span><span id="L-327"><a href="#L-327"><span class="linenos">327</span></a><span class="sd">		concept_set_item_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each mapping</span>
+</span><span id="L-328"><a href="#L-328"><span class="linenos">328</span></a><span class="sd">		concept_set_id INTEGER NOT NULL,                      -- Foreign key to CONCEPT_SET table</span>
+</span><span id="L-329"><a href="#L-329"><span class="linenos">329</span></a><span class="sd">		concept_id INTEGER NOT NULL,                          -- Foreign key to CONCEPT table</span>
+</span><span id="L-330"><a href="#L-330"><span class="linenos">330</span></a><span class="sd">		FOREIGN KEY (concept_set_id) REFERENCES CONCEPT_SET(concept_set_id),</span>
+</span><span id="L-331"><a href="#L-331"><span class="linenos">331</span></a><span class="sd">		FOREIGN KEY (concept_id) REFERENCES CONCEPT(concept_id)</span>
+</span><span id="L-332"><a href="#L-332"><span class="linenos">332</span></a><span class="sd">	);&quot;&quot;&quot;</span>
+</span><span id="L-333"><a href="#L-333"><span class="linenos">333</span></a>    <span class="p">)</span>
+</span><span id="L-334"><a href="#L-334"><span class="linenos">334</span></a>
+</span><span id="L-335"><a href="#L-335"><span class="linenos">335</span></a>    <span class="c1"># read map files</span>
+</span><span id="L-336"><a href="#L-336"><span class="linenos">336</span></a>    <span class="n">map_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
+</span><span id="L-337"><a href="#L-337"><span class="linenos">337</span></a>    <span class="n">total</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">map_files</span><span class="p">)</span>
+</span><span id="L-338"><a href="#L-338"><span class="linenos">338</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Exporting </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2"> map files&quot;</span><span class="p">)</span>
+</span><span id="L-339"><a href="#L-339"><span class="linenos">339</span></a>    <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">map_file</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">map_files</span><span class="p">):</span>
+</span><span id="L-340"><a href="#L-340"><span class="linenos">340</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Processing </span><span class="si">{</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">map_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="L-341"><a href="#L-341"><span class="linenos">341</span></a>        <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">map_file</span><span class="p">)</span>
+</span><span id="L-342"><a href="#L-342"><span class="linenos">342</span></a>
+</span><span id="L-343"><a href="#L-343"><span class="linenos">343</span></a>        <span class="k">for</span> <span class="n">concept_set_name</span><span class="p">,</span> <span class="n">grp</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">&quot;CONCEPT_SET&quot;</span><span class="p">):</span>
+</span><span id="L-344"><a href="#L-344"><span class="linenos">344</span></a>            <span class="c1"># create Concept_Set</span>
+</span><span id="L-345"><a href="#L-345"><span class="linenos">345</span></a>            <span class="k">if</span> <span class="ow">not</span> <span class="n">concept_set_exist</span><span class="p">(</span><span class="n">cur</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">concept_set_name</span><span class="p">)):</span>
+</span><span id="L-346"><a href="#L-346"><span class="linenos">346</span></a>                <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-347"><a href="#L-347"><span class="linenos">347</span></a>                    <span class="sa">f</span><span class="s2">&quot;INSERT INTO CONCEPT_SET (concept_set_name, vocabulary_id) VALUES (&#39;</span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2">&#39;, &#39;</span><span class="si">{</span><span class="n">omop_metadata</span><span class="p">[</span><span class="s1">&#39;vocabulary_id&#39;</span><span class="p">]</span><span class="si">}</span><span class="s2">&#39;);&quot;</span>
+</span><span id="L-348"><a href="#L-348"><span class="linenos">348</span></a>                <span class="p">)</span>
+</span><span id="L-349"><a href="#L-349"><span class="linenos">349</span></a>            <span class="k">else</span><span class="p">:</span>
+</span><span id="L-350"><a href="#L-350"><span class="linenos">350</span></a>                <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Concept_set </span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2"> already exists&quot;</span><span class="p">)</span>
+</span><span id="L-351"><a href="#L-351"><span class="linenos">351</span></a>                <span class="c1"># TODO: ask to remove old concept_set?</span>
+</span><span id="L-352"><a href="#L-352"><span class="linenos">352</span></a>
+</span><span id="L-353"><a href="#L-353"><span class="linenos">353</span></a>            <span class="c1"># get Concept_set_Id</span>
+</span><span id="L-354"><a href="#L-354"><span class="linenos">354</span></a>            <span class="n">query</span> <span class="o">=</span> <span class="s2">&quot;SELECT concept_set_id FROM CONCEPT_SET WHERE concept_set_name = ? AND vocabulary_id = ?;&quot;</span>
+</span><span id="L-355"><a href="#L-355"><span class="linenos">355</span></a>            <span class="n">target_code_type</span> <span class="o">=</span> <span class="n">map_file</span><span class="o">.</span><span class="n">stem</span>
+</span><span id="L-356"><a href="#L-356"><span class="linenos">356</span></a>            <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-357"><a href="#L-357"><span class="linenos">357</span></a>                <span class="n">query</span><span class="p">,</span>
+</span><span id="L-358"><a href="#L-358"><span class="linenos">358</span></a>                <span class="p">(</span>
+</span><span id="L-359"><a href="#L-359"><span class="linenos">359</span></a>                    <span class="n">concept_set_name</span><span class="p">,</span>
+</span><span id="L-360"><a href="#L-360"><span class="linenos">360</span></a>                    <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_id&quot;</span><span class="p">],</span>
+</span><span id="L-361"><a href="#L-361"><span class="linenos">361</span></a>                <span class="p">),</span>
+</span><span id="L-362"><a href="#L-362"><span class="linenos">362</span></a>            <span class="p">)</span>
+</span><span id="L-363"><a href="#L-363"><span class="linenos">363</span></a>            <span class="c1"># FAILS HERE WITH NONE REUR</span>
+</span><span id="L-364"><a href="#L-364"><span class="linenos">364</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="L-365"><a href="#L-365"><span class="linenos">365</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;omop code type </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="L-366"><a href="#L-366"><span class="linenos">366</span></a>            <span class="n">concept_set_id</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="L-367"><a href="#L-367"><span class="linenos">367</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;concept set id </span><span class="si">{</span><span class="n">concept_set_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="L-368"><a href="#L-368"><span class="linenos">368</span></a>
+</span><span id="L-369"><a href="#L-369"><span class="linenos">369</span></a>            <span class="c1"># get corresponing Concept_id (OMOP) for each Concept_code (e.g. SNOMED)</span>
+</span><span id="L-370"><a href="#L-370"><span class="linenos">370</span></a>            <span class="n">concept_codes</span> <span class="o">=</span> <span class="s2">&quot;&#39;&quot;</span> <span class="o">+</span> <span class="s2">&quot;&#39;, &#39;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">grp</span><span class="p">[</span><span class="s2">&quot;CONCEPT&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)))</span> <span class="o">+</span> <span class="s2">&quot;&#39;&quot;</span>
+</span><span id="L-371"><a href="#L-371"><span class="linenos">371</span></a>            <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;SELECT concept_id FROM CONCEPT WHERE vocabulary_id = ? AND concept_code IN (</span><span class="si">{</span><span class="n">concept_codes</span><span class="si">}</span><span class="s2">);&quot;</span>
+</span><span id="L-372"><a href="#L-372"><span class="linenos">372</span></a>            <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">],))</span>
+</span><span id="L-373"><a href="#L-373"><span class="linenos">373</span></a>            <span class="n">df_out</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">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">(),</span> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;concept_id&quot;</span><span class="p">])</span>
+</span><span id="L-374"><a href="#L-374"><span class="linenos">374</span></a>
+</span><span id="L-375"><a href="#L-375"><span class="linenos">375</span></a>            <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">grp</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">df_out</span><span class="p">):</span>
+</span><span id="L-376"><a href="#L-376"><span class="linenos">376</span></a>                <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
+</span><span id="L-377"><a href="#L-377"><span class="linenos">377</span></a>                    <span class="sa">f</span><span class="s2">&quot;ERROR: Some </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2"> Codes do not exist in OMOP Database&quot;</span>
+</span><span id="L-378"><a href="#L-378"><span class="linenos">378</span></a>                <span class="p">)</span>
+</span><span id="L-379"><a href="#L-379"><span class="linenos">379</span></a>
+</span><span id="L-380"><a href="#L-380"><span class="linenos">380</span></a>            <span class="c1"># Create Concept_set_item</span>
+</span><span id="L-381"><a href="#L-381"><span class="linenos">381</span></a>            <span class="n">df_out</span><span class="p">[</span><span class="s2">&quot;concept_set_id&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">concept_set_id</span>
+</span><span id="L-382"><a href="#L-382"><span class="linenos">382</span></a>            <span class="n">df_out</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">&quot;CONCEPT_SET_ITEM&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;append&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-383"><a href="#L-383"><span class="linenos">383</span></a>
+</span><span id="L-384"><a href="#L-384"><span class="linenos">384</span></a>    <span class="c1"># Output all tables to CSV</span>
+</span><span id="L-385"><a href="#L-385"><span class="linenos">385</span></a>    <span class="c1"># Get the list of all tables</span>
+</span><span id="L-386"><a href="#L-386"><span class="linenos">386</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">&quot;SELECT name FROM sqlite_master WHERE type=&#39;table&#39;;&quot;</span><span class="p">)</span>
+</span><span id="L-387"><a href="#L-387"><span class="linenos">387</span></a>    <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>  <span class="c1"># List of tables</span>
+</span><span id="L-388"><a href="#L-388"><span class="linenos">388</span></a>
+</span><span id="L-389"><a href="#L-389"><span class="linenos">389</span></a>    <span class="c1"># Export each table to a separate CSV file</span>
+</span><span id="L-390"><a href="#L-390"><span class="linenos">390</span></a>    <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">:</span>
+</span><span id="L-391"><a href="#L-391"><span class="linenos">391</span></a>        <span class="n">table_name</span> <span class="o">=</span> <span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="L-392"><a href="#L-392"><span class="linenos">392</span></a>        <span class="c1"># ignore SQLite&#39;s internal system table</span>
+</span><span id="L-393"><a href="#L-393"><span class="linenos">393</span></a>        <span class="k">if</span> <span class="n">table_name</span> <span class="o">!=</span> <span class="s2">&quot;sqlite_sequence&quot;</span><span class="p">:</span>
+</span><span id="L-394"><a href="#L-394"><span class="linenos">394</span></a>            <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql_query</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;SELECT * FROM </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+</span><span id="L-395"><a href="#L-395"><span class="linenos">395</span></a>            <span class="n">output_file</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv&quot;</span>
+</span><span id="L-396"><a href="#L-396"><span class="linenos">396</span></a>            <span class="n">output_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">output_file</span>
+</span><span id="L-397"><a href="#L-397"><span class="linenos">397</span></a>            <span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>  <span class="c1"># Save as CSV</span>
+</span><span id="L-398"><a href="#L-398"><span class="linenos">398</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Exported </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">)</span>
+</span><span id="L-399"><a href="#L-399"><span class="linenos">399</span></a>
+</span><span id="L-400"><a href="#L-400"><span class="linenos">400</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="L-401"><a href="#L-401"><span class="linenos">401</span></a>
+</span><span id="L-402"><a href="#L-402"><span class="linenos">402</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Created export db successfully&quot;</span><span class="p">)</span>
+</span><span id="L-403"><a href="#L-403"><span class="linenos">403</span></a>
+</span><span id="L-404"><a href="#L-404"><span class="linenos">404</span></a>    <span class="k">return</span> <span class="n">export_db_path</span>
 </span></pre></div>
 
 
@@ -585,71 +655,97 @@
 
     </div>
     <a class="headerlink" href="#install"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="install-67"><a href="#install-67"><span class="linenos"> 67</span></a><span class="k">def</span><span class="w"> </span><span class="nf">install</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
-</span><span id="install-68"><a href="#install-68"><span class="linenos"> 68</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Installs the OMOP release csv files in a file-based sql database&quot;&quot;&quot;</span>
-</span><span id="install-69"><a href="#install-69"><span class="linenos"> 69</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Installing OMOP from zip file: </span><span class="si">{</span><span class="n">omop_zip_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="install-70"><a href="#install-70"><span class="linenos"> 70</span></a>    <span class="n">omop_zip_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">)</span>
-</span><span id="install-71"><a href="#install-71"><span class="linenos"> 71</span></a>
-</span><span id="install-72"><a href="#install-72"><span class="linenos"> 72</span></a>    <span class="c1"># Check if the file exists and is a ZIP file</span>
-</span><span id="install-73"><a href="#install-73"><span class="linenos"> 73</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">omop_zip_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
-</span><span id="install-74"><a href="#install-74"><span class="linenos"> 74</span></a>        <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> does not exist.&quot;</span>
-</span><span id="install-75"><a href="#install-75"><span class="linenos"> 75</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-</span><span id="install-76"><a href="#install-76"><span class="linenos"> 76</span></a>        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-</span><span id="install-77"><a href="#install-77"><span class="linenos"> 77</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">is_zipfile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">):</span>
-</span><span id="install-78"><a href="#install-78"><span class="linenos"> 78</span></a>        <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;Error: </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> is not a valid ZIP file.&quot;</span>
-</span><span id="install-79"><a href="#install-79"><span class="linenos"> 79</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-</span><span id="install-80"><a href="#install-80"><span class="linenos"> 80</span></a>        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-</span><span id="install-81"><a href="#install-81"><span class="linenos"> 81</span></a>
-</span><span id="install-82"><a href="#install-82"><span class="linenos"> 82</span></a>    <span class="c1"># check codes directory exists and if not create it</span>
-</span><span id="install-83"><a href="#install-83"><span class="linenos"> 83</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
-</span><span id="install-84"><a href="#install-84"><span class="linenos"> 84</span></a>        <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-</span><span id="install-85"><a href="#install-85"><span class="linenos"> 85</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP directory &#39;</span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">&#39; created.&quot;</span><span class="p">)</span>
-</span><span id="install-86"><a href="#install-86"><span class="linenos"> 86</span></a>    <span class="k">else</span><span class="p">:</span>
-</span><span id="install-87"><a href="#install-87"><span class="linenos"> 87</span></a>        <span class="c1"># removing existing OMOP files</span>
-</span><span id="install-88"><a href="#install-88"><span class="linenos"> 88</span></a>        <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
-</span><span id="install-89"><a href="#install-89"><span class="linenos"> 89</span></a>        <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
-</span><span id="install-90"><a href="#install-90"><span class="linenos"> 90</span></a>            <span class="n">file</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
-</span><span id="install-91"><a href="#install-91"><span class="linenos"> 91</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Deleted OMOP csv file: </span><span class="si">{</span><span class="n">file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="install-92"><a href="#install-92"><span class="linenos"> 92</span></a>
-</span><span id="install-93"><a href="#install-93"><span class="linenos"> 93</span></a>    <span class="c1"># Extract ZIP contents</span>
-</span><span id="install-94"><a href="#install-94"><span class="linenos"> 94</span></a>    <span class="k">with</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">zip_ref</span><span class="p">:</span>
-</span><span id="install-95"><a href="#install-95"><span class="linenos"> 95</span></a>        <span class="n">zip_ref</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="p">)</span>
-</span><span id="install-96"><a href="#install-96"><span class="linenos"> 96</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Extracted OMOP zip file </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">/&quot;</span><span class="p">)</span>
-</span><span id="install-97"><a href="#install-97"><span class="linenos"> 97</span></a>
-</span><span id="install-98"><a href="#install-98"><span class="linenos"> 98</span></a>    <span class="c1"># connect to database, if it does not exist it will be created</span>
-</span><span id="install-99"><a href="#install-99"><span class="linenos"> 99</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">)</span>
-</span><span id="install-100"><a href="#install-100"><span class="linenos">100</span></a>
-</span><span id="install-101"><a href="#install-101"><span class="linenos">101</span></a>    <span class="c1"># Iterate through files in the folder</span>
-</span><span id="install-102"><a href="#install-102"><span class="linenos">102</span></a>    <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
-</span><span id="install-103"><a href="#install-103"><span class="linenos">103</span></a>    <span class="n">total_tables_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">csv_files</span><span class="p">)</span>
-</span><span id="install-104"><a href="#install-104"><span class="linenos">104</span></a>    <span class="n">table_count</span> <span class="o">=</span> <span class="mi">1</span>
-</span><span id="install-105"><a href="#install-105"><span class="linenos">105</span></a>    <span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
-</span><span id="install-106"><a href="#install-106"><span class="linenos">106</span></a>        <span class="k">try</span><span class="p">:</span>
-</span><span id="install-107"><a href="#install-107"><span class="linenos">107</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
-</span><span id="install-108"><a href="#install-108"><span class="linenos">108</span></a>                <span class="sa">f</span><span class="s2">&quot;Processing </span><span class="si">{</span><span class="n">table_count</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total_tables_count</span><span class="si">}</span><span class="s2"> tables: </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">&quot;</span>
-</span><span id="install-109"><a href="#install-109"><span class="linenos">109</span></a>            <span class="p">)</span>
-</span><span id="install-110"><a href="#install-110"><span class="linenos">110</span></a>            <span class="c1"># read the CSV file with the specified delimiter</span>
-</span><span id="install-111"><a href="#install-111"><span class="linenos">111</span></a>            <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">low_memory</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-</span><span id="install-112"><a href="#install-112"><span class="linenos">112</span></a>
-</span><span id="install-113"><a href="#install-113"><span class="linenos">113</span></a>            <span class="c1"># export Table to sqlite db</span>
-</span><span id="install-114"><a href="#install-114"><span class="linenos">114</span></a>            <span class="n">df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;replace&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-</span><span id="install-115"><a href="#install-115"><span class="linenos">115</span></a>
-</span><span id="install-116"><a href="#install-116"><span class="linenos">116</span></a>            <span class="c1"># add to the metadata</span>
-</span><span id="install-117"><a href="#install-117"><span class="linenos">117</span></a>            <span class="nb">list</span><span class="p">(</span><span class="n">vocabularies</span><span class="p">[</span><span class="s2">&quot;tables&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">)</span>
-</span><span id="install-118"><a href="#install-118"><span class="linenos">118</span></a>            <span class="n">table_count</span> <span class="o">=</span> <span class="n">table_count</span> <span class="o">+</span> <span class="mi">1</span>
-</span><span id="install-119"><a href="#install-119"><span class="linenos">119</span></a>        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
-</span><span id="install-120"><a href="#install-120"><span class="linenos">120</span></a>            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error reading file </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="install-121"><a href="#install-121"><span class="linenos">121</span></a>
-</span><span id="install-122"><a href="#install-122"><span class="linenos">122</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</span><span id="install-123"><a href="#install-123"><span class="linenos">123</span></a>
-</span><span id="install-124"><a href="#install-124"><span class="linenos">124</span></a>    <span class="c1"># write version file</span>
-</span><span id="install-125"><a href="#install-125"><span class="linenos">125</span></a>    <span class="n">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
-</span><span id="install-126"><a href="#install-126"><span class="linenos">126</span></a>
-</span><span id="install-127"><a href="#install-127"><span class="linenos">127</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP installation completed&quot;</span><span class="p">)</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="install-66"><a href="#install-66"><span class="linenos"> 66</span></a><span class="k">def</span><span class="w"> </span><span class="nf">install</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="install-67"><a href="#install-67"><span class="linenos"> 67</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;&quot;Installs the OMOP release csv files in a file-based sql database</span>
+</span><span id="install-68"><a href="#install-68"><span class="linenos"> 68</span></a>
+</span><span id="install-69"><a href="#install-69"><span class="linenos"> 69</span></a><span class="sd">    Args:</span>
+</span><span id="install-70"><a href="#install-70"><span class="linenos"> 70</span></a><span class="sd">        omop_zip_file (str): vocabularies zip file distributed by OHDSI Athena</span>
+</span><span id="install-71"><a href="#install-71"><span class="linenos"> 71</span></a><span class="sd">        version (str): version of the vocabularies distributed by OHDSI Athena</span>
+</span><span id="install-72"><a href="#install-72"><span class="linenos"> 72</span></a>
+</span><span id="install-73"><a href="#install-73"><span class="linenos"> 73</span></a><span class="sd">    Raises:</span>
+</span><span id="install-74"><a href="#install-74"><span class="linenos"> 74</span></a><span class="sd">        ValueError: if the zip file does not exist</span>
+</span><span id="install-75"><a href="#install-75"><span class="linenos"> 75</span></a><span class="sd">        ValueError: if the file is not a zip file</span>
+</span><span id="install-76"><a href="#install-76"><span class="linenos"> 76</span></a><span class="sd">        Exception: if error reading omop csv files</span>
+</span><span id="install-77"><a href="#install-77"><span class="linenos"> 77</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="install-78"><a href="#install-78"><span class="linenos"> 78</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Installing OMOP from zip file: </span><span class="si">{</span><span class="n">omop_zip_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="install-79"><a href="#install-79"><span class="linenos"> 79</span></a>    <span class="n">omop_zip_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">)</span>
+</span><span id="install-80"><a href="#install-80"><span class="linenos"> 80</span></a>
+</span><span id="install-81"><a href="#install-81"><span class="linenos"> 81</span></a>    <span class="c1"># Check if the file exists and is a ZIP file</span>
+</span><span id="install-82"><a href="#install-82"><span class="linenos"> 82</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">omop_zip_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="install-83"><a href="#install-83"><span class="linenos"> 83</span></a>        <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> does not exist.&quot;</span>
+</span><span id="install-84"><a href="#install-84"><span class="linenos"> 84</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="install-85"><a href="#install-85"><span class="linenos"> 85</span></a>        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="install-86"><a href="#install-86"><span class="linenos"> 86</span></a>    
+</span><span id="install-87"><a href="#install-87"><span class="linenos"> 87</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">is_zipfile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">):</span>
+</span><span id="install-88"><a href="#install-88"><span class="linenos"> 88</span></a>        <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;Error: </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> is not a valid ZIP file.&quot;</span>
+</span><span id="install-89"><a href="#install-89"><span class="linenos"> 89</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="install-90"><a href="#install-90"><span class="linenos"> 90</span></a>        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="install-91"><a href="#install-91"><span class="linenos"> 91</span></a>
+</span><span id="install-92"><a href="#install-92"><span class="linenos"> 92</span></a>    <span class="c1"># check codes directory exists and if not create it</span>
+</span><span id="install-93"><a href="#install-93"><span class="linenos"> 93</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="install-94"><a href="#install-94"><span class="linenos"> 94</span></a>        <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="install-95"><a href="#install-95"><span class="linenos"> 95</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP directory &#39;</span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">&#39; created.&quot;</span><span class="p">)</span>
+</span><span id="install-96"><a href="#install-96"><span class="linenos"> 96</span></a>    <span class="k">else</span><span class="p">:</span>
+</span><span id="install-97"><a href="#install-97"><span class="linenos"> 97</span></a>        <span class="c1"># removing existing OMOP files</span>
+</span><span id="install-98"><a href="#install-98"><span class="linenos"> 98</span></a>        <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
+</span><span id="install-99"><a href="#install-99"><span class="linenos"> 99</span></a>        <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
+</span><span id="install-100"><a href="#install-100"><span class="linenos">100</span></a>            <span class="n">file</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="install-101"><a href="#install-101"><span class="linenos">101</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Deleted OMOP csv file: </span><span class="si">{</span><span class="n">file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="install-102"><a href="#install-102"><span class="linenos">102</span></a>
+</span><span id="install-103"><a href="#install-103"><span class="linenos">103</span></a>    <span class="c1"># Extract ZIP contents</span>
+</span><span id="install-104"><a href="#install-104"><span class="linenos">104</span></a>    <span class="k">with</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">zip_ref</span><span class="p">:</span>
+</span><span id="install-105"><a href="#install-105"><span class="linenos">105</span></a>        <span class="n">zip_ref</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="p">)</span>
+</span><span id="install-106"><a href="#install-106"><span class="linenos">106</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Extracted OMOP zip file </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">/&quot;</span><span class="p">)</span>
+</span><span id="install-107"><a href="#install-107"><span class="linenos">107</span></a>
+</span><span id="install-108"><a href="#install-108"><span class="linenos">108</span></a>    <span class="c1"># connect to database, if it does not exist it will be created</span>
+</span><span id="install-109"><a href="#install-109"><span class="linenos">109</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">)</span>
+</span><span id="install-110"><a href="#install-110"><span class="linenos">110</span></a>
+</span><span id="install-111"><a href="#install-111"><span class="linenos">111</span></a>    <span class="c1"># Iterate through files in the folder</span>
+</span><span id="install-112"><a href="#install-112"><span class="linenos">112</span></a>    <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
+</span><span id="install-113"><a href="#install-113"><span class="linenos">113</span></a>    <span class="n">total_tables_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">csv_files</span><span class="p">)</span>
+</span><span id="install-114"><a href="#install-114"><span class="linenos">114</span></a>    <span class="n">table_count</span> <span class="o">=</span> <span class="mi">1</span>
+</span><span id="install-115"><a href="#install-115"><span class="linenos">115</span></a>    <span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
+</span><span id="install-116"><a href="#install-116"><span class="linenos">116</span></a>        <span class="k">try</span><span class="p">:</span>
+</span><span id="install-117"><a href="#install-117"><span class="linenos">117</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="install-118"><a href="#install-118"><span class="linenos">118</span></a>                <span class="sa">f</span><span class="s2">&quot;Processing </span><span class="si">{</span><span class="n">table_count</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total_tables_count</span><span class="si">}</span><span class="s2"> tables: </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">&quot;</span>
+</span><span id="install-119"><a href="#install-119"><span class="linenos">119</span></a>            <span class="p">)</span>
+</span><span id="install-120"><a href="#install-120"><span class="linenos">120</span></a>            <span class="c1"># read the CSV file with the specified delimiter</span>
+</span><span id="install-121"><a href="#install-121"><span class="linenos">121</span></a>            <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">low_memory</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="install-122"><a href="#install-122"><span class="linenos">122</span></a>
+</span><span id="install-123"><a href="#install-123"><span class="linenos">123</span></a>            <span class="c1"># export Table to sqlite db</span>
+</span><span id="install-124"><a href="#install-124"><span class="linenos">124</span></a>            <span class="n">df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;replace&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="install-125"><a href="#install-125"><span class="linenos">125</span></a>
+</span><span id="install-126"><a href="#install-126"><span class="linenos">126</span></a>            <span class="c1"># add to the metadata</span>
+</span><span id="install-127"><a href="#install-127"><span class="linenos">127</span></a>            <span class="nb">list</span><span class="p">(</span><span class="n">vocabularies</span><span class="p">[</span><span class="s2">&quot;tables&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">)</span>
+</span><span id="install-128"><a href="#install-128"><span class="linenos">128</span></a>            <span class="n">table_count</span> <span class="o">=</span> <span class="n">table_count</span> <span class="o">+</span> <span class="mi">1</span>
+</span><span id="install-129"><a href="#install-129"><span class="linenos">129</span></a>        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="install-130"><a href="#install-130"><span class="linenos">130</span></a>            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error reading file </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="install-131"><a href="#install-131"><span class="linenos">131</span></a>
+</span><span id="install-132"><a href="#install-132"><span class="linenos">132</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="install-133"><a href="#install-133"><span class="linenos">133</span></a>
+</span><span id="install-134"><a href="#install-134"><span class="linenos">134</span></a>    <span class="c1"># write version file</span>
+</span><span id="install-135"><a href="#install-135"><span class="linenos">135</span></a>    <span class="n">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
+</span><span id="install-136"><a href="#install-136"><span class="linenos">136</span></a>
+</span><span id="install-137"><a href="#install-137"><span class="linenos">137</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP installation completed&quot;</span><span class="p">)</span>
 </span></pre></div>
 
 
-            <div class="docstring"><p>Installs the OMOP release csv files in a file-based sql database</p>
+            <div class="docstring"><p>"Installs the OMOP release csv files in a file-based sql database</p>
+
+<h6 id="arguments">Arguments:</h6>
+
+<ul>
+<li><strong>omop_zip_file (str):</strong>  vocabularies zip file distributed by OHDSI Athena</li>
+<li><strong>version (str):</strong>  version of the vocabularies distributed by OHDSI Athena</li>
+</ul>
+
+<h6 id="raises">Raises:</h6>
+
+<ul>
+<li><strong>ValueError:</strong>  if the zip file does not exist</li>
+<li><strong>ValueError:</strong>  if the file is not a zip file</li>
+<li><strong>Exception:</strong>  if error reading omop csv files</li>
+</ul>
 </div>
 
 
@@ -665,22 +761,32 @@
 
     </div>
     <a class="headerlink" href="#write_version_file"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="write_version_file-130"><a href="#write_version_file-130"><span class="linenos">130</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
-</span><span id="write_version_file-131"><a href="#write_version_file-131"><span class="linenos">131</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Writes the OMOP vocaburaries and version to a file&quot;&quot;&quot;</span>
-</span><span id="write_version_file-132"><a href="#write_version_file-132"><span class="linenos">132</span></a>    <span class="n">vocabularies</span><span class="p">[</span><span class="s2">&quot;version&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">version</span>
-</span><span id="write_version_file-133"><a href="#write_version_file-133"><span class="linenos">133</span></a>    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">VERSION_PATH</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
-</span><span id="write_version_file-134"><a href="#write_version_file-134"><span class="linenos">134</span></a>        <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
-</span><span id="write_version_file-135"><a href="#write_version_file-135"><span class="linenos">135</span></a>            <span class="n">vocabularies</span><span class="p">,</span>
-</span><span id="write_version_file-136"><a href="#write_version_file-136"><span class="linenos">136</span></a>            <span class="n">file</span><span class="p">,</span>
-</span><span id="write_version_file-137"><a href="#write_version_file-137"><span class="linenos">137</span></a>            <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
-</span><span id="write_version_file-138"><a href="#write_version_file-138"><span class="linenos">138</span></a>            <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
-</span><span id="write_version_file-139"><a href="#write_version_file-139"><span class="linenos">139</span></a>            <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
-</span><span id="write_version_file-140"><a href="#write_version_file-140"><span class="linenos">140</span></a>            <span class="n">default_style</span><span class="o">=</span><span class="s1">&#39;&quot;&#39;</span><span class="p">,</span>
-</span><span id="write_version_file-141"><a href="#write_version_file-141"><span class="linenos">141</span></a>        <span class="p">)</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="write_version_file-140"><a href="#write_version_file-140"><span class="linenos">140</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="write_version_file-141"><a href="#write_version_file-141"><span class="linenos">141</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Writes the OMOP vocaburaries and version to a file</span>
+</span><span id="write_version_file-142"><a href="#write_version_file-142"><span class="linenos">142</span></a>
+</span><span id="write_version_file-143"><a href="#write_version_file-143"><span class="linenos">143</span></a><span class="sd">    Args:</span>
+</span><span id="write_version_file-144"><a href="#write_version_file-144"><span class="linenos">144</span></a><span class="sd">        version (str): version of the vocabularies distributed by OHDSI Athena</span>
+</span><span id="write_version_file-145"><a href="#write_version_file-145"><span class="linenos">145</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="write_version_file-146"><a href="#write_version_file-146"><span class="linenos">146</span></a>    <span class="n">vocabularies</span><span class="p">[</span><span class="s2">&quot;version&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">version</span>
+</span><span id="write_version_file-147"><a href="#write_version_file-147"><span class="linenos">147</span></a>    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">VERSION_PATH</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="write_version_file-148"><a href="#write_version_file-148"><span class="linenos">148</span></a>        <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="write_version_file-149"><a href="#write_version_file-149"><span class="linenos">149</span></a>            <span class="n">vocabularies</span><span class="p">,</span>
+</span><span id="write_version_file-150"><a href="#write_version_file-150"><span class="linenos">150</span></a>            <span class="n">file</span><span class="p">,</span>
+</span><span id="write_version_file-151"><a href="#write_version_file-151"><span class="linenos">151</span></a>            <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="write_version_file-152"><a href="#write_version_file-152"><span class="linenos">152</span></a>            <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="write_version_file-153"><a href="#write_version_file-153"><span class="linenos">153</span></a>            <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="write_version_file-154"><a href="#write_version_file-154"><span class="linenos">154</span></a>            <span class="n">default_style</span><span class="o">=</span><span class="s1">&#39;&quot;&#39;</span><span class="p">,</span>
+</span><span id="write_version_file-155"><a href="#write_version_file-155"><span class="linenos">155</span></a>        <span class="p">)</span>
 </span></pre></div>
 
 
             <div class="docstring"><p>Writes the OMOP vocaburaries and version to a file</p>
+
+<h6 id="arguments">Arguments:</h6>
+
+<ul>
+<li><strong>version (str):</strong>  version of the vocabularies distributed by OHDSI Athena</li>
+</ul>
 </div>
 
 
@@ -696,28 +802,47 @@
 
     </div>
     <a class="headerlink" href="#clear"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="clear-144"><a href="#clear-144"><span class="linenos">144</span></a><span class="k">def</span><span class="w"> </span><span class="nf">clear</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
-</span><span id="clear-145"><a href="#clear-145"><span class="linenos">145</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Clears the OMOP sql database&quot;&quot;&quot;</span>
-</span><span id="clear-146"><a href="#clear-146"><span class="linenos">146</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Clearing OMOP data from database&quot;</span><span class="p">)</span>
-</span><span id="clear-147"><a href="#clear-147"><span class="linenos">147</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
-</span><span id="clear-148"><a href="#clear-148"><span class="linenos">148</span></a>        <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error: OMOP DB file &#39;</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">&#39; does not exist.&quot;</span><span class="p">)</span>
-</span><span id="clear-149"><a href="#clear-149"><span class="linenos">149</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db_path</span><span class="p">)</span>
-</span><span id="clear-150"><a href="#clear-150"><span class="linenos">150</span></a>    <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
-</span><span id="clear-151"><a href="#clear-151"><span class="linenos">151</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">&quot;SELECT name FROM sqlite_master WHERE type=&#39;table&#39;;&quot;</span><span class="p">)</span>
-</span><span id="clear-152"><a href="#clear-152"><span class="linenos">152</span></a>
-</span><span id="clear-153"><a href="#clear-153"><span class="linenos">153</span></a>    <span class="c1"># Fetch and print table names</span>
-</span><span id="clear-154"><a href="#clear-154"><span class="linenos">154</span></a>    <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>
-</span><span id="clear-155"><a href="#clear-155"><span class="linenos">155</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Tables in database:&quot;</span><span class="p">,</span> <span class="p">[</span><span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">])</span>
-</span><span id="clear-156"><a href="#clear-156"><span class="linenos">156</span></a>
-</span><span id="clear-157"><a href="#clear-157"><span class="linenos">157</span></a>    <span class="c1"># cur.execute(&quot;DROP TABLE CONCEPT_SET;&quot;)</span>
-</span><span id="clear-158"><a href="#clear-158"><span class="linenos">158</span></a>    <span class="c1"># cur.execute(&quot;DROP TABLE CONCEPT_SET_ITEM;&quot;)</span>
-</span><span id="clear-159"><a href="#clear-159"><span class="linenos">159</span></a>
-</span><span id="clear-160"><a href="#clear-160"><span class="linenos">160</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</span><span id="clear-161"><a href="#clear-161"><span class="linenos">161</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP database cleared&quot;</span><span class="p">)</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="clear-158"><a href="#clear-158"><span class="linenos">158</span></a><span class="k">def</span><span class="w"> </span><span class="nf">clear</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="clear-159"><a href="#clear-159"><span class="linenos">159</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Clears the OMOP sql database</span>
+</span><span id="clear-160"><a href="#clear-160"><span class="linenos">160</span></a>
+</span><span id="clear-161"><a href="#clear-161"><span class="linenos">161</span></a><span class="sd">    Args:</span>
+</span><span id="clear-162"><a href="#clear-162"><span class="linenos">162</span></a><span class="sd">        db_path (Path): the path to the omop sqllite database</span>
+</span><span id="clear-163"><a href="#clear-163"><span class="linenos">163</span></a>
+</span><span id="clear-164"><a href="#clear-164"><span class="linenos">164</span></a><span class="sd">    Raises:</span>
+</span><span id="clear-165"><a href="#clear-165"><span class="linenos">165</span></a><span class="sd">        FileNotFoundError: if the omop sqllite database does not exist</span>
+</span><span id="clear-166"><a href="#clear-166"><span class="linenos">166</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="clear-167"><a href="#clear-167"><span class="linenos">167</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Clearing OMOP data from database&quot;</span><span class="p">)</span>
+</span><span id="clear-168"><a href="#clear-168"><span class="linenos">168</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="clear-169"><a href="#clear-169"><span class="linenos">169</span></a>        <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error: OMOP DB file &#39;</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">&#39; does not exist.&quot;</span><span class="p">)</span>
+</span><span id="clear-170"><a href="#clear-170"><span class="linenos">170</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db_path</span><span class="p">)</span>
+</span><span id="clear-171"><a href="#clear-171"><span class="linenos">171</span></a>    <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="clear-172"><a href="#clear-172"><span class="linenos">172</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">&quot;SELECT name FROM sqlite_master WHERE type=&#39;table&#39;;&quot;</span><span class="p">)</span>
+</span><span id="clear-173"><a href="#clear-173"><span class="linenos">173</span></a>
+</span><span id="clear-174"><a href="#clear-174"><span class="linenos">174</span></a>    <span class="c1"># Fetch and print table names</span>
+</span><span id="clear-175"><a href="#clear-175"><span class="linenos">175</span></a>    <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>
+</span><span id="clear-176"><a href="#clear-176"><span class="linenos">176</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Tables in database:&quot;</span><span class="p">,</span> <span class="p">[</span><span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">])</span>
+</span><span id="clear-177"><a href="#clear-177"><span class="linenos">177</span></a>
+</span><span id="clear-178"><a href="#clear-178"><span class="linenos">178</span></a>    <span class="c1"># cur.execute(&quot;DROP TABLE CONCEPT_SET;&quot;)</span>
+</span><span id="clear-179"><a href="#clear-179"><span class="linenos">179</span></a>    <span class="c1"># cur.execute(&quot;DROP TABLE CONCEPT_SET_ITEM;&quot;)</span>
+</span><span id="clear-180"><a href="#clear-180"><span class="linenos">180</span></a>
+</span><span id="clear-181"><a href="#clear-181"><span class="linenos">181</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="clear-182"><a href="#clear-182"><span class="linenos">182</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP database cleared&quot;</span><span class="p">)</span>
 </span></pre></div>
 
 
             <div class="docstring"><p>Clears the OMOP sql database</p>
+
+<h6 id="arguments">Arguments:</h6>
+
+<ul>
+<li><strong>db_path (Path):</strong>  the path to the omop sqllite database</li>
+</ul>
+
+<h6 id="raises">Raises:</h6>
+
+<ul>
+<li><strong>FileNotFoundError:</strong>  if the omop sqllite database does not exist</li>
+</ul>
 </div>
 
 
@@ -733,18 +858,38 @@
 
     </div>
     <a class="headerlink" href="#delete"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="delete-164"><a href="#delete-164"><span class="linenos">164</span></a><span class="k">def</span><span class="w"> </span><span class="nf">delete</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
-</span><span id="delete-165"><a href="#delete-165"><span class="linenos">165</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Deletes the OMOP sql database&quot;&quot;&quot;</span>
-</span><span id="delete-166"><a href="#delete-166"><span class="linenos">166</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Deleting OMOP database&quot;</span><span class="p">)</span>
-</span><span id="delete-167"><a href="#delete-167"><span class="linenos">167</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
-</span><span id="delete-168"><a href="#delete-168"><span class="linenos">168</span></a>        <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error: OMOP DB file &#39;</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">&#39; does not exist.&quot;</span><span class="p">)</span>
-</span><span id="delete-169"><a href="#delete-169"><span class="linenos">169</span></a>
-</span><span id="delete-170"><a href="#delete-170"><span class="linenos">170</span></a>    <span class="n">db_path</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
-</span><span id="delete-171"><a href="#delete-171"><span class="linenos">171</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP database deleted&quot;</span><span class="p">)</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="delete-185"><a href="#delete-185"><span class="linenos">185</span></a><span class="k">def</span><span class="w"> </span><span class="nf">delete</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="delete-186"><a href="#delete-186"><span class="linenos">186</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Deletes the OMOP sql database</span>
+</span><span id="delete-187"><a href="#delete-187"><span class="linenos">187</span></a>
+</span><span id="delete-188"><a href="#delete-188"><span class="linenos">188</span></a><span class="sd">    Args:</span>
+</span><span id="delete-189"><a href="#delete-189"><span class="linenos">189</span></a><span class="sd">        db_path (Path): the path to the omop sqllite database</span>
+</span><span id="delete-190"><a href="#delete-190"><span class="linenos">190</span></a>
+</span><span id="delete-191"><a href="#delete-191"><span class="linenos">191</span></a><span class="sd">    Raises:</span>
+</span><span id="delete-192"><a href="#delete-192"><span class="linenos">192</span></a><span class="sd">        FileNotFoundError: if the omop sqllite database does not exist</span>
+</span><span id="delete-193"><a href="#delete-193"><span class="linenos">193</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="delete-194"><a href="#delete-194"><span class="linenos">194</span></a>    
+</span><span id="delete-195"><a href="#delete-195"><span class="linenos">195</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Deleting OMOP database&quot;</span><span class="p">)</span>
+</span><span id="delete-196"><a href="#delete-196"><span class="linenos">196</span></a>    <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="delete-197"><a href="#delete-197"><span class="linenos">197</span></a>        <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Error: OMOP DB file &#39;</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">&#39; does not exist.&quot;</span><span class="p">)</span>
+</span><span id="delete-198"><a href="#delete-198"><span class="linenos">198</span></a>
+</span><span id="delete-199"><a href="#delete-199"><span class="linenos">199</span></a>    <span class="n">db_path</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="delete-200"><a href="#delete-200"><span class="linenos">200</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;OMOP database deleted&quot;</span><span class="p">)</span>
 </span></pre></div>
 
 
             <div class="docstring"><p>Deletes the OMOP sql database</p>
+
+<h6 id="arguments">Arguments:</h6>
+
+<ul>
+<li><strong>db_path (Path):</strong>  the path to the omop sqllite database</li>
+</ul>
+
+<h6 id="raises">Raises:</h6>
+
+<ul>
+<li><strong>FileNotFoundError:</strong>  if the omop sqllite database does not exist</li>
+</ul>
 </div>
 
 
@@ -760,25 +905,49 @@
 
     </div>
     <a class="headerlink" href="#table_exists"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="table_exists-174"><a href="#table_exists-174"><span class="linenos">174</span></a><span class="k">def</span><span class="w"> </span><span class="nf">table_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">table_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-</span><span id="table_exists-175"><a href="#table_exists-175"><span class="linenos">175</span></a>    <span class="c1"># Query to check if the table exists</span>
-</span><span id="table_exists-176"><a href="#table_exists-176"><span class="linenos">176</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="table_exists-177"><a href="#table_exists-177"><span class="linenos">177</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-</span><span id="table_exists-178"><a href="#table_exists-178"><span class="linenos">178</span></a><span class="sd">		SELECT name</span>
-</span><span id="table_exists-179"><a href="#table_exists-179"><span class="linenos">179</span></a><span class="sd">		FROM sqlite_master</span>
-</span><span id="table_exists-180"><a href="#table_exists-180"><span class="linenos">180</span></a><span class="sd">		WHERE type=&#39;table&#39; AND name=?</span>
-</span><span id="table_exists-181"><a href="#table_exists-181"><span class="linenos">181</span></a><span class="sd">		&quot;&quot;&quot;</span><span class="p">,</span>
-</span><span id="table_exists-182"><a href="#table_exists-182"><span class="linenos">182</span></a>        <span class="p">(</span><span class="n">table_name</span><span class="p">,),</span>
-</span><span id="table_exists-183"><a href="#table_exists-183"><span class="linenos">183</span></a>    <span class="p">)</span>
-</span><span id="table_exists-184"><a href="#table_exists-184"><span class="linenos">184</span></a>
-</span><span id="table_exists-185"><a href="#table_exists-185"><span class="linenos">185</span></a>    <span class="c1"># Fetch the result</span>
-</span><span id="table_exists-186"><a href="#table_exists-186"><span class="linenos">186</span></a>    <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
-</span><span id="table_exists-187"><a href="#table_exists-187"><span class="linenos">187</span></a>
-</span><span id="table_exists-188"><a href="#table_exists-188"><span class="linenos">188</span></a>    <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="table_exists-203"><a href="#table_exists-203"><span class="linenos">203</span></a><span class="k">def</span><span class="w"> </span><span class="nf">table_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">table_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="table_exists-204"><a href="#table_exists-204"><span class="linenos">204</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Query to check if the table exists</span>
+</span><span id="table_exists-205"><a href="#table_exists-205"><span class="linenos">205</span></a>
+</span><span id="table_exists-206"><a href="#table_exists-206"><span class="linenos">206</span></a><span class="sd">    Args:</span>
+</span><span id="table_exists-207"><a href="#table_exists-207"><span class="linenos">207</span></a><span class="sd">        cursor (sqlite3.Cursor): a sqllite database cursor</span>
+</span><span id="table_exists-208"><a href="#table_exists-208"><span class="linenos">208</span></a><span class="sd">        table_name (str): the table name to check</span>
+</span><span id="table_exists-209"><a href="#table_exists-209"><span class="linenos">209</span></a>
+</span><span id="table_exists-210"><a href="#table_exists-210"><span class="linenos">210</span></a><span class="sd">    Returns:</span>
+</span><span id="table_exists-211"><a href="#table_exists-211"><span class="linenos">211</span></a><span class="sd">        bool: true if table exists</span>
+</span><span id="table_exists-212"><a href="#table_exists-212"><span class="linenos">212</span></a><span class="sd">    &quot;&quot;&quot;</span>    
+</span><span id="table_exists-213"><a href="#table_exists-213"><span class="linenos">213</span></a>        
+</span><span id="table_exists-214"><a href="#table_exists-214"><span class="linenos">214</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="table_exists-215"><a href="#table_exists-215"><span class="linenos">215</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="table_exists-216"><a href="#table_exists-216"><span class="linenos">216</span></a><span class="sd">		SELECT name</span>
+</span><span id="table_exists-217"><a href="#table_exists-217"><span class="linenos">217</span></a><span class="sd">		FROM sqlite_master</span>
+</span><span id="table_exists-218"><a href="#table_exists-218"><span class="linenos">218</span></a><span class="sd">		WHERE type=&#39;table&#39; AND name=?</span>
+</span><span id="table_exists-219"><a href="#table_exists-219"><span class="linenos">219</span></a><span class="sd">		&quot;&quot;&quot;</span><span class="p">,</span>
+</span><span id="table_exists-220"><a href="#table_exists-220"><span class="linenos">220</span></a>        <span class="p">(</span><span class="n">table_name</span><span class="p">,),</span>
+</span><span id="table_exists-221"><a href="#table_exists-221"><span class="linenos">221</span></a>    <span class="p">)</span>
+</span><span id="table_exists-222"><a href="#table_exists-222"><span class="linenos">222</span></a>
+</span><span id="table_exists-223"><a href="#table_exists-223"><span class="linenos">223</span></a>    <span class="c1"># Fetch the result</span>
+</span><span id="table_exists-224"><a href="#table_exists-224"><span class="linenos">224</span></a>    <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+</span><span id="table_exists-225"><a href="#table_exists-225"><span class="linenos">225</span></a>
+</span><span id="table_exists-226"><a href="#table_exists-226"><span class="linenos">226</span></a>    <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
 </span></pre></div>
 
 
-    
+            <div class="docstring"><p>Query to check if the table exists</p>
+
+<h6 id="arguments">Arguments:</h6>
+
+<ul>
+<li><strong>cursor (sqlite3.Cursor):</strong>  a sqllite database cursor</li>
+<li><strong>table_name (str):</strong>  the table name to check</li>
+</ul>
+
+<h6 id="returns">Returns:</h6>
+
+<blockquote>
+  <p>bool: true if table exists</p>
+</blockquote>
+</div>
+
 
                 </section>
                 <section id="vocab_exists">
@@ -792,25 +961,49 @@
 
     </div>
     <a class="headerlink" href="#vocab_exists"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="vocab_exists-191"><a href="#vocab_exists-191"><span class="linenos">191</span></a><span class="k">def</span><span class="w"> </span><span class="nf">vocab_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">vocab_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-</span><span id="vocab_exists-192"><a href="#vocab_exists-192"><span class="linenos">192</span></a>    <span class="c1"># Query to check if the table exists</span>
-</span><span id="vocab_exists-193"><a href="#vocab_exists-193"><span class="linenos">193</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="vocab_exists-194"><a href="#vocab_exists-194"><span class="linenos">194</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-</span><span id="vocab_exists-195"><a href="#vocab_exists-195"><span class="linenos">195</span></a><span class="sd">		SELECT vocabulary_id </span>
-</span><span id="vocab_exists-196"><a href="#vocab_exists-196"><span class="linenos">196</span></a><span class="sd">		FROM VOCABULARY</span>
-</span><span id="vocab_exists-197"><a href="#vocab_exists-197"><span class="linenos">197</span></a><span class="sd">		WHERE vocabulary_id=?</span>
-</span><span id="vocab_exists-198"><a href="#vocab_exists-198"><span class="linenos">198</span></a><span class="sd">		&quot;&quot;&quot;</span><span class="p">,</span>
-</span><span id="vocab_exists-199"><a href="#vocab_exists-199"><span class="linenos">199</span></a>        <span class="p">(</span><span class="n">vocab_id</span><span class="p">,),</span>
-</span><span id="vocab_exists-200"><a href="#vocab_exists-200"><span class="linenos">200</span></a>    <span class="p">)</span>
-</span><span id="vocab_exists-201"><a href="#vocab_exists-201"><span class="linenos">201</span></a>
-</span><span id="vocab_exists-202"><a href="#vocab_exists-202"><span class="linenos">202</span></a>    <span class="c1"># Fetch the result</span>
-</span><span id="vocab_exists-203"><a href="#vocab_exists-203"><span class="linenos">203</span></a>    <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
-</span><span id="vocab_exists-204"><a href="#vocab_exists-204"><span class="linenos">204</span></a>
-</span><span id="vocab_exists-205"><a href="#vocab_exists-205"><span class="linenos">205</span></a>    <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="vocab_exists-229"><a href="#vocab_exists-229"><span class="linenos">229</span></a><span class="k">def</span><span class="w"> </span><span class="nf">vocab_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">vocab_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="vocab_exists-230"><a href="#vocab_exists-230"><span class="linenos">230</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Query to check if the vocabulary exists</span>
+</span><span id="vocab_exists-231"><a href="#vocab_exists-231"><span class="linenos">231</span></a>
+</span><span id="vocab_exists-232"><a href="#vocab_exists-232"><span class="linenos">232</span></a><span class="sd">    Args:</span>
+</span><span id="vocab_exists-233"><a href="#vocab_exists-233"><span class="linenos">233</span></a><span class="sd">        cursor (sqlite3.Cursor): a sqllite database cursor</span>
+</span><span id="vocab_exists-234"><a href="#vocab_exists-234"><span class="linenos">234</span></a><span class="sd">        vocab_id (str): the vocabulary id to check</span>
+</span><span id="vocab_exists-235"><a href="#vocab_exists-235"><span class="linenos">235</span></a>
+</span><span id="vocab_exists-236"><a href="#vocab_exists-236"><span class="linenos">236</span></a><span class="sd">    Returns:</span>
+</span><span id="vocab_exists-237"><a href="#vocab_exists-237"><span class="linenos">237</span></a><span class="sd">        bool: true if vocabulary id exists</span>
+</span><span id="vocab_exists-238"><a href="#vocab_exists-238"><span class="linenos">238</span></a><span class="sd">    &quot;&quot;&quot;</span>    
+</span><span id="vocab_exists-239"><a href="#vocab_exists-239"><span class="linenos">239</span></a>    
+</span><span id="vocab_exists-240"><a href="#vocab_exists-240"><span class="linenos">240</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="vocab_exists-241"><a href="#vocab_exists-241"><span class="linenos">241</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="vocab_exists-242"><a href="#vocab_exists-242"><span class="linenos">242</span></a><span class="sd">		SELECT vocabulary_id </span>
+</span><span id="vocab_exists-243"><a href="#vocab_exists-243"><span class="linenos">243</span></a><span class="sd">		FROM VOCABULARY</span>
+</span><span id="vocab_exists-244"><a href="#vocab_exists-244"><span class="linenos">244</span></a><span class="sd">		WHERE vocabulary_id=?</span>
+</span><span id="vocab_exists-245"><a href="#vocab_exists-245"><span class="linenos">245</span></a><span class="sd">		&quot;&quot;&quot;</span><span class="p">,</span>
+</span><span id="vocab_exists-246"><a href="#vocab_exists-246"><span class="linenos">246</span></a>        <span class="p">(</span><span class="n">vocab_id</span><span class="p">,),</span>
+</span><span id="vocab_exists-247"><a href="#vocab_exists-247"><span class="linenos">247</span></a>    <span class="p">)</span>
+</span><span id="vocab_exists-248"><a href="#vocab_exists-248"><span class="linenos">248</span></a>
+</span><span id="vocab_exists-249"><a href="#vocab_exists-249"><span class="linenos">249</span></a>    <span class="c1"># Fetch the result</span>
+</span><span id="vocab_exists-250"><a href="#vocab_exists-250"><span class="linenos">250</span></a>    <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+</span><span id="vocab_exists-251"><a href="#vocab_exists-251"><span class="linenos">251</span></a>
+</span><span id="vocab_exists-252"><a href="#vocab_exists-252"><span class="linenos">252</span></a>    <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
 </span></pre></div>
 
 
-    
+            <div class="docstring"><p>Query to check if the vocabulary exists</p>
+
+<h6 id="arguments">Arguments:</h6>
+
+<ul>
+<li><strong>cursor (sqlite3.Cursor):</strong>  a sqllite database cursor</li>
+<li><strong>vocab_id (str):</strong>  the vocabulary id to check</li>
+</ul>
+
+<h6 id="returns">Returns:</h6>
+
+<blockquote>
+  <p>bool: true if vocabulary id exists</p>
+</blockquote>
+</div>
+
 
                 </section>
                 <section id="concept_set_exist">
@@ -824,16 +1017,41 @@
 
     </div>
     <a class="headerlink" href="#concept_set_exist"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="concept_set_exist-208"><a href="#concept_set_exist-208"><span class="linenos">208</span></a><span class="k">def</span><span class="w"> </span><span class="nf">concept_set_exist</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">concept_set_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
-</span><span id="concept_set_exist-209"><a href="#concept_set_exist-209"><span class="linenos">209</span></a>    <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;SELECT EXISTS (SELECT 1 FROM CONCEPT_SET WHERE concept_set_name = ?)&quot;</span>
-</span><span id="concept_set_exist-210"><a href="#concept_set_exist-210"><span class="linenos">210</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">concept_set_name</span><span class="p">,))</span>
-</span><span id="concept_set_exist-211"><a href="#concept_set_exist-211"><span class="linenos">211</span></a>
-</span><span id="concept_set_exist-212"><a href="#concept_set_exist-212"><span class="linenos">212</span></a>    <span class="c1"># 1 if exists, 0 otherwise</span>
-</span><span id="concept_set_exist-213"><a href="#concept_set_exist-213"><span class="linenos">213</span></a>    <span class="k">return</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="concept_set_exist-255"><a href="#concept_set_exist-255"><span class="linenos">255</span></a><span class="k">def</span><span class="w"> </span><span class="nf">concept_set_exist</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">concept_set_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="concept_set_exist-256"><a href="#concept_set_exist-256"><span class="linenos">256</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Query to check if the concept set exists</span>
+</span><span id="concept_set_exist-257"><a href="#concept_set_exist-257"><span class="linenos">257</span></a>
+</span><span id="concept_set_exist-258"><a href="#concept_set_exist-258"><span class="linenos">258</span></a><span class="sd">    Args:</span>
+</span><span id="concept_set_exist-259"><a href="#concept_set_exist-259"><span class="linenos">259</span></a><span class="sd">        cursor (sqlite3.Cursor): a sqllite database cursor</span>
+</span><span id="concept_set_exist-260"><a href="#concept_set_exist-260"><span class="linenos">260</span></a><span class="sd">        concept_set_name (str): the concept set name to check</span>
+</span><span id="concept_set_exist-261"><a href="#concept_set_exist-261"><span class="linenos">261</span></a>
+</span><span id="concept_set_exist-262"><a href="#concept_set_exist-262"><span class="linenos">262</span></a><span class="sd">    Returns:</span>
+</span><span id="concept_set_exist-263"><a href="#concept_set_exist-263"><span class="linenos">263</span></a><span class="sd">        bool: true if concept set exists</span>
+</span><span id="concept_set_exist-264"><a href="#concept_set_exist-264"><span class="linenos">264</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="concept_set_exist-265"><a href="#concept_set_exist-265"><span class="linenos">265</span></a>    
+</span><span id="concept_set_exist-266"><a href="#concept_set_exist-266"><span class="linenos">266</span></a>    <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;SELECT EXISTS (SELECT 1 FROM CONCEPT_SET WHERE concept_set_name = ?)&quot;</span>
+</span><span id="concept_set_exist-267"><a href="#concept_set_exist-267"><span class="linenos">267</span></a>    <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">concept_set_name</span><span class="p">,))</span>
+</span><span id="concept_set_exist-268"><a href="#concept_set_exist-268"><span class="linenos">268</span></a>
+</span><span id="concept_set_exist-269"><a href="#concept_set_exist-269"><span class="linenos">269</span></a>    <span class="c1"># 1 if exists, 0 otherwise</span>
+</span><span id="concept_set_exist-270"><a href="#concept_set_exist-270"><span class="linenos">270</span></a>    <span class="k">return</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span>
 </span></pre></div>
 
 
-    
+            <div class="docstring"><p>Query to check if the concept set exists</p>
+
+<h6 id="arguments">Arguments:</h6>
+
+<ul>
+<li><strong>cursor (sqlite3.Cursor):</strong>  a sqllite database cursor</li>
+<li><strong>concept_set_name (str):</strong>  the concept set name to check</li>
+</ul>
+
+<h6 id="returns">Returns:</h6>
+
+<blockquote>
+  <p>bool: true if concept set exists</p>
+</blockquote>
+</div>
+
 
                 </section>
                 <section id="export">
@@ -841,136 +1059,166 @@
 <div class="attr function">
             
         <span class="def">def</span>
-        <span class="name">export</span><span class="signature pdoc-code multiline">(<span class="param">	<span class="n">map_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>,</span><span class="param">	<span class="n">export_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>,</span><span class="param">	<span class="n">version</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param">	<span class="n">omop_metadata</span></span><span class="return-annotation">) -> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>:</span></span>
+        <span class="name">export</span><span class="signature pdoc-code multiline">(<span class="param">	<span class="n">map_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>,</span><span class="param">	<span class="n">export_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>,</span><span class="param">	<span class="n">version</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param">	<span class="n">omop_metadata</span><span class="p">:</span> <span class="nb">dict</span></span><span class="return-annotation">) -> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>:</span></span>
 
                 <label class="view-source-button" for="export-view-source"><span>View Source</span></label>
 
     </div>
     <a class="headerlink" href="#export"></a>
-            <div class="pdoc-code codehilite"><pre><span></span><span id="export-216"><a href="#export-216"><span class="linenos">216</span></a><span class="k">def</span><span class="w"> </span><span class="nf">export</span><span class="p">(</span><span class="n">map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">export_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">omop_metadata</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Path</span><span class="p">:</span>
-</span><span id="export-217"><a href="#export-217"><span class="linenos">217</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;exporting with metadata </span><span class="si">{</span><span class="n">omop_metadata</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="export-218"><a href="#export-218"><span class="linenos">218</span></a>
-</span><span id="export-219"><a href="#export-219"><span class="linenos">219</span></a>    <span class="c1"># copy the baseline omop database</span>
-</span><span id="export-220"><a href="#export-220"><span class="linenos">220</span></a>    <span class="n">export_db_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">EXPORT_FILE</span>
-</span><span id="export-221"><a href="#export-221"><span class="linenos">221</span></a>    <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">,</span> <span class="n">export_db_path</span><span class="p">)</span>
-</span><span id="export-222"><a href="#export-222"><span class="linenos">222</span></a>
-</span><span id="export-223"><a href="#export-223"><span class="linenos">223</span></a>    <span class="c1"># connect to db</span>
-</span><span id="export-224"><a href="#export-224"><span class="linenos">224</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">export_db_path</span><span class="p">)</span>
-</span><span id="export-225"><a href="#export-225"><span class="linenos">225</span></a>    <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
-</span><span id="export-226"><a href="#export-226"><span class="linenos">226</span></a>
-</span><span id="export-227"><a href="#export-227"><span class="linenos">227</span></a>    <span class="c1"># Create VOCABULARY</span>
-</span><span id="export-228"><a href="#export-228"><span class="linenos">228</span></a>    <span class="n">df_test</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
-</span><span id="export-229"><a href="#export-229"><span class="linenos">229</span></a>        <span class="p">[</span>
-</span><span id="export-230"><a href="#export-230"><span class="linenos">230</span></a>            <span class="p">{</span>
-</span><span id="export-231"><a href="#export-231"><span class="linenos">231</span></a>                <span class="s2">&quot;vocabulary_id&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_id&quot;</span><span class="p">],</span>
-</span><span id="export-232"><a href="#export-232"><span class="linenos">232</span></a>                <span class="s2">&quot;vocabulary_name&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_name&quot;</span><span class="p">],</span>
-</span><span id="export-233"><a href="#export-233"><span class="linenos">233</span></a>                <span class="s2">&quot;vocabulary_reference&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_reference&quot;</span><span class="p">],</span>
-</span><span id="export-234"><a href="#export-234"><span class="linenos">234</span></a>                <span class="s2">&quot;vocabulary_version&quot;</span><span class="p">:</span> <span class="n">version</span><span class="p">,</span>
-</span><span id="export-235"><a href="#export-235"><span class="linenos">235</span></a>                <span class="c1"># &quot;vocabulary_concept_id&quot;: 0,</span>
-</span><span id="export-236"><a href="#export-236"><span class="linenos">236</span></a>            <span class="p">}</span>
-</span><span id="export-237"><a href="#export-237"><span class="linenos">237</span></a>        <span class="p">]</span>
-</span><span id="export-238"><a href="#export-238"><span class="linenos">238</span></a>    <span class="p">)</span>
-</span><span id="export-239"><a href="#export-239"><span class="linenos">239</span></a>    <span class="n">df_test</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">&quot;VOCABULARY&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;append&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-</span><span id="export-240"><a href="#export-240"><span class="linenos">240</span></a>
-</span><span id="export-241"><a href="#export-241"><span class="linenos">241</span></a>    <span class="c1"># Create CONCEPT_SET</span>
-</span><span id="export-242"><a href="#export-242"><span class="linenos">242</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="export-243"><a href="#export-243"><span class="linenos">243</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-</span><span id="export-244"><a href="#export-244"><span class="linenos">244</span></a><span class="sd">	CREATE TABLE CONCEPT_SET (</span>
-</span><span id="export-245"><a href="#export-245"><span class="linenos">245</span></a><span class="sd">		concept_set_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each concept set</span>
-</span><span id="export-246"><a href="#export-246"><span class="linenos">246</span></a><span class="sd">		atlas_id INTEGER,                                -- Unique identifier generated by ATLAS</span>
-</span><span id="export-247"><a href="#export-247"><span class="linenos">247</span></a><span class="sd">		concept_set_name TEXT,                           -- Optional name for the concept set</span>
-</span><span id="export-248"><a href="#export-248"><span class="linenos">248</span></a><span class="sd">		concept_set_description TEXT,                    -- Optional description for the concept set</span>
-</span><span id="export-249"><a href="#export-249"><span class="linenos">249</span></a><span class="sd">		vocabulary_id TEXT NOT NULL,                     -- Foreign key to VOCABULARY table</span>
-</span><span id="export-250"><a href="#export-250"><span class="linenos">250</span></a><span class="sd">		FOREIGN KEY (vocabulary_id) REFERENCES VOCABULARY(vocabulary_id)</span>
-</span><span id="export-251"><a href="#export-251"><span class="linenos">251</span></a><span class="sd">	);&quot;&quot;&quot;</span>
-</span><span id="export-252"><a href="#export-252"><span class="linenos">252</span></a>    <span class="p">)</span>
-</span><span id="export-253"><a href="#export-253"><span class="linenos">253</span></a>
-</span><span id="export-254"><a href="#export-254"><span class="linenos">254</span></a>    <span class="c1"># Create CONCEPT_SET_ITEM</span>
-</span><span id="export-255"><a href="#export-255"><span class="linenos">255</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="export-256"><a href="#export-256"><span class="linenos">256</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
-</span><span id="export-257"><a href="#export-257"><span class="linenos">257</span></a><span class="sd">	CREATE TABLE CONCEPT_SET_ITEM (</span>
-</span><span id="export-258"><a href="#export-258"><span class="linenos">258</span></a><span class="sd">		concept_set_item_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each mapping</span>
-</span><span id="export-259"><a href="#export-259"><span class="linenos">259</span></a><span class="sd">		concept_set_id INTEGER NOT NULL,                      -- Foreign key to CONCEPT_SET table</span>
-</span><span id="export-260"><a href="#export-260"><span class="linenos">260</span></a><span class="sd">		concept_id INTEGER NOT NULL,                          -- Foreign key to CONCEPT table</span>
-</span><span id="export-261"><a href="#export-261"><span class="linenos">261</span></a><span class="sd">		FOREIGN KEY (concept_set_id) REFERENCES CONCEPT_SET(concept_set_id),</span>
-</span><span id="export-262"><a href="#export-262"><span class="linenos">262</span></a><span class="sd">		FOREIGN KEY (concept_id) REFERENCES CONCEPT(concept_id)</span>
-</span><span id="export-263"><a href="#export-263"><span class="linenos">263</span></a><span class="sd">	);&quot;&quot;&quot;</span>
-</span><span id="export-264"><a href="#export-264"><span class="linenos">264</span></a>    <span class="p">)</span>
-</span><span id="export-265"><a href="#export-265"><span class="linenos">265</span></a>
-</span><span id="export-266"><a href="#export-266"><span class="linenos">266</span></a>    <span class="c1"># read map files</span>
-</span><span id="export-267"><a href="#export-267"><span class="linenos">267</span></a>    <span class="n">map_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
-</span><span id="export-268"><a href="#export-268"><span class="linenos">268</span></a>    <span class="n">total</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">map_files</span><span class="p">)</span>
-</span><span id="export-269"><a href="#export-269"><span class="linenos">269</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Exporting </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2"> map files&quot;</span><span class="p">)</span>
-</span><span id="export-270"><a href="#export-270"><span class="linenos">270</span></a>    <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">map_file</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">map_files</span><span class="p">):</span>
-</span><span id="export-271"><a href="#export-271"><span class="linenos">271</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Processing </span><span class="si">{</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">map_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="export-272"><a href="#export-272"><span class="linenos">272</span></a>        <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">map_file</span><span class="p">)</span>
-</span><span id="export-273"><a href="#export-273"><span class="linenos">273</span></a>
-</span><span id="export-274"><a href="#export-274"><span class="linenos">274</span></a>        <span class="k">for</span> <span class="n">concept_set_name</span><span class="p">,</span> <span class="n">grp</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">&quot;CONCEPT_SET&quot;</span><span class="p">):</span>
-</span><span id="export-275"><a href="#export-275"><span class="linenos">275</span></a>            <span class="c1"># create Concept_Set</span>
-</span><span id="export-276"><a href="#export-276"><span class="linenos">276</span></a>            <span class="k">if</span> <span class="ow">not</span> <span class="n">concept_set_exist</span><span class="p">(</span><span class="n">cur</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">concept_set_name</span><span class="p">)):</span>
-</span><span id="export-277"><a href="#export-277"><span class="linenos">277</span></a>                <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="export-278"><a href="#export-278"><span class="linenos">278</span></a>                    <span class="sa">f</span><span class="s2">&quot;INSERT INTO CONCEPT_SET (concept_set_name, vocabulary_id) VALUES (&#39;</span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2">&#39;, &#39;</span><span class="si">{</span><span class="n">omop_metadata</span><span class="p">[</span><span class="s1">&#39;vocabulary_id&#39;</span><span class="p">]</span><span class="si">}</span><span class="s2">&#39;);&quot;</span>
-</span><span id="export-279"><a href="#export-279"><span class="linenos">279</span></a>                <span class="p">)</span>
-</span><span id="export-280"><a href="#export-280"><span class="linenos">280</span></a>            <span class="k">else</span><span class="p">:</span>
-</span><span id="export-281"><a href="#export-281"><span class="linenos">281</span></a>                <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Concept_set </span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2"> already exists&quot;</span><span class="p">)</span>
-</span><span id="export-282"><a href="#export-282"><span class="linenos">282</span></a>                <span class="c1"># TODO: ask to remove old concept_set?</span>
-</span><span id="export-283"><a href="#export-283"><span class="linenos">283</span></a>
-</span><span id="export-284"><a href="#export-284"><span class="linenos">284</span></a>            <span class="c1"># get Concept_set_Id</span>
-</span><span id="export-285"><a href="#export-285"><span class="linenos">285</span></a>            <span class="n">query</span> <span class="o">=</span> <span class="s2">&quot;SELECT concept_set_id FROM CONCEPT_SET WHERE concept_set_name = ? AND vocabulary_id = ?;&quot;</span>
-</span><span id="export-286"><a href="#export-286"><span class="linenos">286</span></a>            <span class="n">target_code_type</span> <span class="o">=</span> <span class="n">map_file</span><span class="o">.</span><span class="n">stem</span>
-</span><span id="export-287"><a href="#export-287"><span class="linenos">287</span></a>            <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
-</span><span id="export-288"><a href="#export-288"><span class="linenos">288</span></a>                <span class="n">query</span><span class="p">,</span>
-</span><span id="export-289"><a href="#export-289"><span class="linenos">289</span></a>                <span class="p">(</span>
-</span><span id="export-290"><a href="#export-290"><span class="linenos">290</span></a>                    <span class="n">concept_set_name</span><span class="p">,</span>
-</span><span id="export-291"><a href="#export-291"><span class="linenos">291</span></a>                    <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_id&quot;</span><span class="p">],</span>
-</span><span id="export-292"><a href="#export-292"><span class="linenos">292</span></a>                <span class="p">),</span>
-</span><span id="export-293"><a href="#export-293"><span class="linenos">293</span></a>            <span class="p">)</span>
-</span><span id="export-294"><a href="#export-294"><span class="linenos">294</span></a>            <span class="c1"># FAILS HERE WITH NONE REUR</span>
-</span><span id="export-295"><a href="#export-295"><span class="linenos">295</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="export-296"><a href="#export-296"><span class="linenos">296</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;omop code type </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="export-297"><a href="#export-297"><span class="linenos">297</span></a>            <span class="n">concept_set_id</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
-</span><span id="export-298"><a href="#export-298"><span class="linenos">298</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;concept set id </span><span class="si">{</span><span class="n">concept_set_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-</span><span id="export-299"><a href="#export-299"><span class="linenos">299</span></a>
-</span><span id="export-300"><a href="#export-300"><span class="linenos">300</span></a>            <span class="c1"># get corresponing Concept_id (OMOP) for each Concept_code (e.g. SNOMED)</span>
-</span><span id="export-301"><a href="#export-301"><span class="linenos">301</span></a>            <span class="n">concept_codes</span> <span class="o">=</span> <span class="s2">&quot;&#39;&quot;</span> <span class="o">+</span> <span class="s2">&quot;&#39;, &#39;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">grp</span><span class="p">[</span><span class="s2">&quot;CONCEPT&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)))</span> <span class="o">+</span> <span class="s2">&quot;&#39;&quot;</span>
-</span><span id="export-302"><a href="#export-302"><span class="linenos">302</span></a>            <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;SELECT concept_id FROM CONCEPT WHERE vocabulary_id = ? AND concept_code IN (</span><span class="si">{</span><span class="n">concept_codes</span><span class="si">}</span><span class="s2">);&quot;</span>
-</span><span id="export-303"><a href="#export-303"><span class="linenos">303</span></a>            <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">],))</span>
-</span><span id="export-304"><a href="#export-304"><span class="linenos">304</span></a>            <span class="n">df_out</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">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">(),</span> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;concept_id&quot;</span><span class="p">])</span>
-</span><span id="export-305"><a href="#export-305"><span class="linenos">305</span></a>
-</span><span id="export-306"><a href="#export-306"><span class="linenos">306</span></a>            <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">grp</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">df_out</span><span class="p">):</span>
-</span><span id="export-307"><a href="#export-307"><span class="linenos">307</span></a>                <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
-</span><span id="export-308"><a href="#export-308"><span class="linenos">308</span></a>                    <span class="sa">f</span><span class="s2">&quot;ERROR: Some </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2"> Codes do not exist in OMOP Database&quot;</span>
-</span><span id="export-309"><a href="#export-309"><span class="linenos">309</span></a>                <span class="p">)</span>
+            <div class="pdoc-code codehilite"><pre><span></span><span id="export-273"><a href="#export-273"><span class="linenos">273</span></a><span class="k">def</span><span class="w"> </span><span class="nf">export</span><span class="p">(</span><span class="n">map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">export_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">omop_metadata</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Path</span><span class="p">:</span>
+</span><span id="export-274"><a href="#export-274"><span class="linenos">274</span></a><span class="w">    </span><span class="sd">&quot;&quot;&quot;Export concept sets to omop database in csv format</span>
+</span><span id="export-275"><a href="#export-275"><span class="linenos">275</span></a>
+</span><span id="export-276"><a href="#export-276"><span class="linenos">276</span></a><span class="sd">    Args:</span>
+</span><span id="export-277"><a href="#export-277"><span class="linenos">277</span></a><span class="sd">        map_path (Path): path to the acmc map directory containing concept sets in csv format</span>
+</span><span id="export-278"><a href="#export-278"><span class="linenos">278</span></a><span class="sd">        export_path (Path): path to the directory where the omop database csv files are to be written</span>
+</span><span id="export-279"><a href="#export-279"><span class="linenos">279</span></a><span class="sd">        version (str): phenotype version for omop vocabulary version</span>
+</span><span id="export-280"><a href="#export-280"><span class="linenos">280</span></a><span class="sd">        omop_metadata (dict): phenotype omop metadata for omop vocabulary metadata </span>
+</span><span id="export-281"><a href="#export-281"><span class="linenos">281</span></a><span class="sd">                </span>
+</span><span id="export-282"><a href="#export-282"><span class="linenos">282</span></a><span class="sd">    Returns:</span>
+</span><span id="export-283"><a href="#export-283"><span class="linenos">283</span></a><span class="sd">        Path: path to the exported sqllite database</span>
+</span><span id="export-284"><a href="#export-284"><span class="linenos">284</span></a><span class="sd">    &quot;&quot;&quot;</span>
+</span><span id="export-285"><a href="#export-285"><span class="linenos">285</span></a>    
+</span><span id="export-286"><a href="#export-286"><span class="linenos">286</span></a>    
+</span><span id="export-287"><a href="#export-287"><span class="linenos">287</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;exporting with metadata </span><span class="si">{</span><span class="n">omop_metadata</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="export-288"><a href="#export-288"><span class="linenos">288</span></a>
+</span><span id="export-289"><a href="#export-289"><span class="linenos">289</span></a>    <span class="c1"># copy the baseline omop database</span>
+</span><span id="export-290"><a href="#export-290"><span class="linenos">290</span></a>    <span class="n">export_db_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">EXPORT_FILE</span>
+</span><span id="export-291"><a href="#export-291"><span class="linenos">291</span></a>    <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">,</span> <span class="n">export_db_path</span><span class="p">)</span>
+</span><span id="export-292"><a href="#export-292"><span class="linenos">292</span></a>
+</span><span id="export-293"><a href="#export-293"><span class="linenos">293</span></a>    <span class="c1"># connect to db</span>
+</span><span id="export-294"><a href="#export-294"><span class="linenos">294</span></a>    <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">export_db_path</span><span class="p">)</span>
+</span><span id="export-295"><a href="#export-295"><span class="linenos">295</span></a>    <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="export-296"><a href="#export-296"><span class="linenos">296</span></a>
+</span><span id="export-297"><a href="#export-297"><span class="linenos">297</span></a>    <span class="c1"># Create VOCABULARY</span>
+</span><span id="export-298"><a href="#export-298"><span class="linenos">298</span></a>    <span class="n">df_test</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="export-299"><a href="#export-299"><span class="linenos">299</span></a>        <span class="p">[</span>
+</span><span id="export-300"><a href="#export-300"><span class="linenos">300</span></a>            <span class="p">{</span>
+</span><span id="export-301"><a href="#export-301"><span class="linenos">301</span></a>                <span class="s2">&quot;vocabulary_id&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_id&quot;</span><span class="p">],</span>
+</span><span id="export-302"><a href="#export-302"><span class="linenos">302</span></a>                <span class="s2">&quot;vocabulary_name&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_name&quot;</span><span class="p">],</span>
+</span><span id="export-303"><a href="#export-303"><span class="linenos">303</span></a>                <span class="s2">&quot;vocabulary_reference&quot;</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_reference&quot;</span><span class="p">],</span>
+</span><span id="export-304"><a href="#export-304"><span class="linenos">304</span></a>                <span class="s2">&quot;vocabulary_version&quot;</span><span class="p">:</span> <span class="n">version</span><span class="p">,</span>
+</span><span id="export-305"><a href="#export-305"><span class="linenos">305</span></a>                <span class="c1"># &quot;vocabulary_concept_id&quot;: 0,</span>
+</span><span id="export-306"><a href="#export-306"><span class="linenos">306</span></a>            <span class="p">}</span>
+</span><span id="export-307"><a href="#export-307"><span class="linenos">307</span></a>        <span class="p">]</span>
+</span><span id="export-308"><a href="#export-308"><span class="linenos">308</span></a>    <span class="p">)</span>
+</span><span id="export-309"><a href="#export-309"><span class="linenos">309</span></a>    <span class="n">df_test</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">&quot;VOCABULARY&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;append&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
 </span><span id="export-310"><a href="#export-310"><span class="linenos">310</span></a>
-</span><span id="export-311"><a href="#export-311"><span class="linenos">311</span></a>            <span class="c1"># Create Concept_set_item</span>
-</span><span id="export-312"><a href="#export-312"><span class="linenos">312</span></a>            <span class="n">df_out</span><span class="p">[</span><span class="s2">&quot;concept_set_id&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">concept_set_id</span>
-</span><span id="export-313"><a href="#export-313"><span class="linenos">313</span></a>            <span class="n">df_out</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">&quot;CONCEPT_SET_ITEM&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;append&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-</span><span id="export-314"><a href="#export-314"><span class="linenos">314</span></a>
-</span><span id="export-315"><a href="#export-315"><span class="linenos">315</span></a>    <span class="c1"># Output all tables to CSV</span>
-</span><span id="export-316"><a href="#export-316"><span class="linenos">316</span></a>    <span class="c1"># Get the list of all tables</span>
-</span><span id="export-317"><a href="#export-317"><span class="linenos">317</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">&quot;SELECT name FROM sqlite_master WHERE type=&#39;table&#39;;&quot;</span><span class="p">)</span>
-</span><span id="export-318"><a href="#export-318"><span class="linenos">318</span></a>    <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>  <span class="c1"># List of tables</span>
-</span><span id="export-319"><a href="#export-319"><span class="linenos">319</span></a>
-</span><span id="export-320"><a href="#export-320"><span class="linenos">320</span></a>    <span class="c1"># Export each table to a separate CSV file</span>
-</span><span id="export-321"><a href="#export-321"><span class="linenos">321</span></a>    <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">:</span>
-</span><span id="export-322"><a href="#export-322"><span class="linenos">322</span></a>        <span class="n">table_name</span> <span class="o">=</span> <span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-</span><span id="export-323"><a href="#export-323"><span class="linenos">323</span></a>        <span class="c1"># ignore SQLite&#39;s internal system table</span>
-</span><span id="export-324"><a href="#export-324"><span class="linenos">324</span></a>        <span class="k">if</span> <span class="n">table_name</span> <span class="o">!=</span> <span class="s2">&quot;sqlite_sequence&quot;</span><span class="p">:</span>
-</span><span id="export-325"><a href="#export-325"><span class="linenos">325</span></a>            <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql_query</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;SELECT * FROM </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
-</span><span id="export-326"><a href="#export-326"><span class="linenos">326</span></a>            <span class="n">output_file</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv&quot;</span>
-</span><span id="export-327"><a href="#export-327"><span class="linenos">327</span></a>            <span class="n">output_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">output_file</span>
-</span><span id="export-328"><a href="#export-328"><span class="linenos">328</span></a>            <span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>  <span class="c1"># Save as CSV</span>
-</span><span id="export-329"><a href="#export-329"><span class="linenos">329</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Exported </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">)</span>
-</span><span id="export-330"><a href="#export-330"><span class="linenos">330</span></a>
-</span><span id="export-331"><a href="#export-331"><span class="linenos">331</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</span><span id="export-332"><a href="#export-332"><span class="linenos">332</span></a>
-</span><span id="export-333"><a href="#export-333"><span class="linenos">333</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Created export db successfully&quot;</span><span class="p">)</span>
-</span><span id="export-334"><a href="#export-334"><span class="linenos">334</span></a>
-</span><span id="export-335"><a href="#export-335"><span class="linenos">335</span></a>    <span class="k">return</span> <span class="n">export_db_path</span>
+</span><span id="export-311"><a href="#export-311"><span class="linenos">311</span></a>    <span class="c1"># Create CONCEPT_SET</span>
+</span><span id="export-312"><a href="#export-312"><span class="linenos">312</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="export-313"><a href="#export-313"><span class="linenos">313</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="export-314"><a href="#export-314"><span class="linenos">314</span></a><span class="sd">	CREATE TABLE CONCEPT_SET (</span>
+</span><span id="export-315"><a href="#export-315"><span class="linenos">315</span></a><span class="sd">		concept_set_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each concept set</span>
+</span><span id="export-316"><a href="#export-316"><span class="linenos">316</span></a><span class="sd">		atlas_id INTEGER,                                -- Unique identifier generated by ATLAS</span>
+</span><span id="export-317"><a href="#export-317"><span class="linenos">317</span></a><span class="sd">		concept_set_name TEXT,                           -- Optional name for the concept set</span>
+</span><span id="export-318"><a href="#export-318"><span class="linenos">318</span></a><span class="sd">		concept_set_description TEXT,                    -- Optional description for the concept set</span>
+</span><span id="export-319"><a href="#export-319"><span class="linenos">319</span></a><span class="sd">		vocabulary_id TEXT NOT NULL,                     -- Foreign key to VOCABULARY table</span>
+</span><span id="export-320"><a href="#export-320"><span class="linenos">320</span></a><span class="sd">		FOREIGN KEY (vocabulary_id) REFERENCES VOCABULARY(vocabulary_id)</span>
+</span><span id="export-321"><a href="#export-321"><span class="linenos">321</span></a><span class="sd">	);&quot;&quot;&quot;</span>
+</span><span id="export-322"><a href="#export-322"><span class="linenos">322</span></a>    <span class="p">)</span>
+</span><span id="export-323"><a href="#export-323"><span class="linenos">323</span></a>
+</span><span id="export-324"><a href="#export-324"><span class="linenos">324</span></a>    <span class="c1"># Create CONCEPT_SET_ITEM</span>
+</span><span id="export-325"><a href="#export-325"><span class="linenos">325</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="export-326"><a href="#export-326"><span class="linenos">326</span></a><span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+</span><span id="export-327"><a href="#export-327"><span class="linenos">327</span></a><span class="sd">	CREATE TABLE CONCEPT_SET_ITEM (</span>
+</span><span id="export-328"><a href="#export-328"><span class="linenos">328</span></a><span class="sd">		concept_set_item_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each mapping</span>
+</span><span id="export-329"><a href="#export-329"><span class="linenos">329</span></a><span class="sd">		concept_set_id INTEGER NOT NULL,                      -- Foreign key to CONCEPT_SET table</span>
+</span><span id="export-330"><a href="#export-330"><span class="linenos">330</span></a><span class="sd">		concept_id INTEGER NOT NULL,                          -- Foreign key to CONCEPT table</span>
+</span><span id="export-331"><a href="#export-331"><span class="linenos">331</span></a><span class="sd">		FOREIGN KEY (concept_set_id) REFERENCES CONCEPT_SET(concept_set_id),</span>
+</span><span id="export-332"><a href="#export-332"><span class="linenos">332</span></a><span class="sd">		FOREIGN KEY (concept_id) REFERENCES CONCEPT(concept_id)</span>
+</span><span id="export-333"><a href="#export-333"><span class="linenos">333</span></a><span class="sd">	);&quot;&quot;&quot;</span>
+</span><span id="export-334"><a href="#export-334"><span class="linenos">334</span></a>    <span class="p">)</span>
+</span><span id="export-335"><a href="#export-335"><span class="linenos">335</span></a>
+</span><span id="export-336"><a href="#export-336"><span class="linenos">336</span></a>    <span class="c1"># read map files</span>
+</span><span id="export-337"><a href="#export-337"><span class="linenos">337</span></a>    <span class="n">map_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
+</span><span id="export-338"><a href="#export-338"><span class="linenos">338</span></a>    <span class="n">total</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">map_files</span><span class="p">)</span>
+</span><span id="export-339"><a href="#export-339"><span class="linenos">339</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Exporting </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2"> map files&quot;</span><span class="p">)</span>
+</span><span id="export-340"><a href="#export-340"><span class="linenos">340</span></a>    <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">map_file</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">map_files</span><span class="p">):</span>
+</span><span id="export-341"><a href="#export-341"><span class="linenos">341</span></a>        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Processing </span><span class="si">{</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">map_file</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="export-342"><a href="#export-342"><span class="linenos">342</span></a>        <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">map_file</span><span class="p">)</span>
+</span><span id="export-343"><a href="#export-343"><span class="linenos">343</span></a>
+</span><span id="export-344"><a href="#export-344"><span class="linenos">344</span></a>        <span class="k">for</span> <span class="n">concept_set_name</span><span class="p">,</span> <span class="n">grp</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">&quot;CONCEPT_SET&quot;</span><span class="p">):</span>
+</span><span id="export-345"><a href="#export-345"><span class="linenos">345</span></a>            <span class="c1"># create Concept_Set</span>
+</span><span id="export-346"><a href="#export-346"><span class="linenos">346</span></a>            <span class="k">if</span> <span class="ow">not</span> <span class="n">concept_set_exist</span><span class="p">(</span><span class="n">cur</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">concept_set_name</span><span class="p">)):</span>
+</span><span id="export-347"><a href="#export-347"><span class="linenos">347</span></a>                <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="export-348"><a href="#export-348"><span class="linenos">348</span></a>                    <span class="sa">f</span><span class="s2">&quot;INSERT INTO CONCEPT_SET (concept_set_name, vocabulary_id) VALUES (&#39;</span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2">&#39;, &#39;</span><span class="si">{</span><span class="n">omop_metadata</span><span class="p">[</span><span class="s1">&#39;vocabulary_id&#39;</span><span class="p">]</span><span class="si">}</span><span class="s2">&#39;);&quot;</span>
+</span><span id="export-349"><a href="#export-349"><span class="linenos">349</span></a>                <span class="p">)</span>
+</span><span id="export-350"><a href="#export-350"><span class="linenos">350</span></a>            <span class="k">else</span><span class="p">:</span>
+</span><span id="export-351"><a href="#export-351"><span class="linenos">351</span></a>                <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Concept_set </span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2"> already exists&quot;</span><span class="p">)</span>
+</span><span id="export-352"><a href="#export-352"><span class="linenos">352</span></a>                <span class="c1"># TODO: ask to remove old concept_set?</span>
+</span><span id="export-353"><a href="#export-353"><span class="linenos">353</span></a>
+</span><span id="export-354"><a href="#export-354"><span class="linenos">354</span></a>            <span class="c1"># get Concept_set_Id</span>
+</span><span id="export-355"><a href="#export-355"><span class="linenos">355</span></a>            <span class="n">query</span> <span class="o">=</span> <span class="s2">&quot;SELECT concept_set_id FROM CONCEPT_SET WHERE concept_set_name = ? AND vocabulary_id = ?;&quot;</span>
+</span><span id="export-356"><a href="#export-356"><span class="linenos">356</span></a>            <span class="n">target_code_type</span> <span class="o">=</span> <span class="n">map_file</span><span class="o">.</span><span class="n">stem</span>
+</span><span id="export-357"><a href="#export-357"><span class="linenos">357</span></a>            <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="export-358"><a href="#export-358"><span class="linenos">358</span></a>                <span class="n">query</span><span class="p">,</span>
+</span><span id="export-359"><a href="#export-359"><span class="linenos">359</span></a>                <span class="p">(</span>
+</span><span id="export-360"><a href="#export-360"><span class="linenos">360</span></a>                    <span class="n">concept_set_name</span><span class="p">,</span>
+</span><span id="export-361"><a href="#export-361"><span class="linenos">361</span></a>                    <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">&quot;vocabulary_id&quot;</span><span class="p">],</span>
+</span><span id="export-362"><a href="#export-362"><span class="linenos">362</span></a>                <span class="p">),</span>
+</span><span id="export-363"><a href="#export-363"><span class="linenos">363</span></a>            <span class="p">)</span>
+</span><span id="export-364"><a href="#export-364"><span class="linenos">364</span></a>            <span class="c1"># FAILS HERE WITH NONE REUR</span>
+</span><span id="export-365"><a href="#export-365"><span class="linenos">365</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="export-366"><a href="#export-366"><span class="linenos">366</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;omop code type </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="export-367"><a href="#export-367"><span class="linenos">367</span></a>            <span class="n">concept_set_id</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="export-368"><a href="#export-368"><span class="linenos">368</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;concept set id </span><span class="si">{</span><span class="n">concept_set_id</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+</span><span id="export-369"><a href="#export-369"><span class="linenos">369</span></a>
+</span><span id="export-370"><a href="#export-370"><span class="linenos">370</span></a>            <span class="c1"># get corresponing Concept_id (OMOP) for each Concept_code (e.g. SNOMED)</span>
+</span><span id="export-371"><a href="#export-371"><span class="linenos">371</span></a>            <span class="n">concept_codes</span> <span class="o">=</span> <span class="s2">&quot;&#39;&quot;</span> <span class="o">+</span> <span class="s2">&quot;&#39;, &#39;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">grp</span><span class="p">[</span><span class="s2">&quot;CONCEPT&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)))</span> <span class="o">+</span> <span class="s2">&quot;&#39;&quot;</span>
+</span><span id="export-372"><a href="#export-372"><span class="linenos">372</span></a>            <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;SELECT concept_id FROM CONCEPT WHERE vocabulary_id = ? AND concept_code IN (</span><span class="si">{</span><span class="n">concept_codes</span><span class="si">}</span><span class="s2">);&quot;</span>
+</span><span id="export-373"><a href="#export-373"><span class="linenos">373</span></a>            <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">],))</span>
+</span><span id="export-374"><a href="#export-374"><span class="linenos">374</span></a>            <span class="n">df_out</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">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">(),</span> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;concept_id&quot;</span><span class="p">])</span>
+</span><span id="export-375"><a href="#export-375"><span class="linenos">375</span></a>
+</span><span id="export-376"><a href="#export-376"><span class="linenos">376</span></a>            <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">grp</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">df_out</span><span class="p">):</span>
+</span><span id="export-377"><a href="#export-377"><span class="linenos">377</span></a>                <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
+</span><span id="export-378"><a href="#export-378"><span class="linenos">378</span></a>                    <span class="sa">f</span><span class="s2">&quot;ERROR: Some </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2"> Codes do not exist in OMOP Database&quot;</span>
+</span><span id="export-379"><a href="#export-379"><span class="linenos">379</span></a>                <span class="p">)</span>
+</span><span id="export-380"><a href="#export-380"><span class="linenos">380</span></a>
+</span><span id="export-381"><a href="#export-381"><span class="linenos">381</span></a>            <span class="c1"># Create Concept_set_item</span>
+</span><span id="export-382"><a href="#export-382"><span class="linenos">382</span></a>            <span class="n">df_out</span><span class="p">[</span><span class="s2">&quot;concept_set_id&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">concept_set_id</span>
+</span><span id="export-383"><a href="#export-383"><span class="linenos">383</span></a>            <span class="n">df_out</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">&quot;CONCEPT_SET_ITEM&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">&quot;append&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="export-384"><a href="#export-384"><span class="linenos">384</span></a>
+</span><span id="export-385"><a href="#export-385"><span class="linenos">385</span></a>    <span class="c1"># Output all tables to CSV</span>
+</span><span id="export-386"><a href="#export-386"><span class="linenos">386</span></a>    <span class="c1"># Get the list of all tables</span>
+</span><span id="export-387"><a href="#export-387"><span class="linenos">387</span></a>    <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">&quot;SELECT name FROM sqlite_master WHERE type=&#39;table&#39;;&quot;</span><span class="p">)</span>
+</span><span id="export-388"><a href="#export-388"><span class="linenos">388</span></a>    <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>  <span class="c1"># List of tables</span>
+</span><span id="export-389"><a href="#export-389"><span class="linenos">389</span></a>
+</span><span id="export-390"><a href="#export-390"><span class="linenos">390</span></a>    <span class="c1"># Export each table to a separate CSV file</span>
+</span><span id="export-391"><a href="#export-391"><span class="linenos">391</span></a>    <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">:</span>
+</span><span id="export-392"><a href="#export-392"><span class="linenos">392</span></a>        <span class="n">table_name</span> <span class="o">=</span> <span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="export-393"><a href="#export-393"><span class="linenos">393</span></a>        <span class="c1"># ignore SQLite&#39;s internal system table</span>
+</span><span id="export-394"><a href="#export-394"><span class="linenos">394</span></a>        <span class="k">if</span> <span class="n">table_name</span> <span class="o">!=</span> <span class="s2">&quot;sqlite_sequence&quot;</span><span class="p">:</span>
+</span><span id="export-395"><a href="#export-395"><span class="linenos">395</span></a>            <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql_query</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;SELECT * FROM </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+</span><span id="export-396"><a href="#export-396"><span class="linenos">396</span></a>            <span class="n">output_file</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv&quot;</span>
+</span><span id="export-397"><a href="#export-397"><span class="linenos">397</span></a>            <span class="n">output_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">output_file</span>
+</span><span id="export-398"><a href="#export-398"><span class="linenos">398</span></a>            <span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>  <span class="c1"># Save as CSV</span>
+</span><span id="export-399"><a href="#export-399"><span class="linenos">399</span></a>            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Exported </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">)</span>
+</span><span id="export-400"><a href="#export-400"><span class="linenos">400</span></a>
+</span><span id="export-401"><a href="#export-401"><span class="linenos">401</span></a>    <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="export-402"><a href="#export-402"><span class="linenos">402</span></a>
+</span><span id="export-403"><a href="#export-403"><span class="linenos">403</span></a>    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Created export db successfully&quot;</span><span class="p">)</span>
+</span><span id="export-404"><a href="#export-404"><span class="linenos">404</span></a>
+</span><span id="export-405"><a href="#export-405"><span class="linenos">405</span></a>    <span class="k">return</span> <span class="n">export_db_path</span>
 </span></pre></div>
 
 
-    
+            <div class="docstring"><p>Export concept sets to omop database in csv format</p>
+
+<h6 id="arguments">Arguments:</h6>
+
+<ul>
+<li><strong>map_path (Path):</strong>  path to the acmc map directory containing concept sets in csv format</li>
+<li><strong>export_path (Path):</strong>  path to the directory where the omop database csv files are to be written</li>
+<li><strong>version (str):</strong>  phenotype version for omop vocabulary version</li>
+<li><strong>omop_metadata (dict):</strong>  phenotype omop metadata for omop vocabulary metadata </li>
+</ul>
+
+<h6 id="returns">Returns:</h6>
+
+<blockquote>
+  <p>Path: path to the exported sqllite database</p>
+</blockquote>
+</div>
+
 
                 </section>
     </main>
diff --git a/docs/api/acmc/parse.html b/docs/api/acmc/parse.html
index 3064df146a591e044af9c5312dc6bca1e806fb05..0ac93e2d6cbfd7ae20e8d4f1ed3a6a12a11b8332 100644
--- a/docs/api/acmc/parse.html
+++ b/docs/api/acmc/parse.html
@@ -765,7 +765,7 @@
                 <section id="SUPPORTED_CODE_TYPES">
                     <div class="attr variable">
             <span class="name">SUPPORTED_CODE_TYPES</span>        =
-<span class="default_value">{&#39;read2&#39;, &#39;icd10&#39;, &#39;atc&#39;, &#39;snomed&#39;, &#39;read3&#39;, &#39;opcs4&#39;}</span>
+<span class="default_value">{&#39;snomed&#39;, &#39;opcs4&#39;, &#39;read2&#39;, &#39;icd10&#39;, &#39;atc&#39;, &#39;read3&#39;}</span>
 
         
     </div>
diff --git a/docs/api/acmc/phen.html b/docs/api/acmc/phen.html
index e9b2d9f7608c678fb6158d31ecb72c0d986ad371..1b41d42f735cf20bd7c7281df26cecf4d26d645a 100644
--- a/docs/api/acmc/phen.html
+++ b/docs/api/acmc/phen.html
@@ -1907,7 +1907,7 @@
                     <div class="attr variable">
             <span class="name">CONFIG_SCHEMA</span>        =
 <input id="CONFIG_SCHEMA-view-value" class="view-value-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
-            <label class="view-value-button pdoc-button" for="CONFIG_SCHEMA-view-value"></label><span class="default_value">{&#39;phenotype&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: True, &#39;schema&#39;: {&#39;version&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True, &#39;regex&#39;: &#39;^\\d+\\.\\d+\\.\\d+$&#39;}, &#39;omop&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: True, &#39;schema&#39;: {&#39;vocabulary_id&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True}, &#39;vocabulary_name&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True}, &#39;vocabulary_reference&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True, &#39;regex&#39;: &#39;^https?://.*&#39;}}}, &#39;map&#39;: {&#39;type&#39;: &#39;list&#39;, &#39;schema&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;allowed&#39;: [&#39;read2&#39;, &#39;icd10&#39;, &#39;atc&#39;, &#39;snomed&#39;, &#39;read3&#39;, &#39;opcs4&#39;]}}, &#39;concept_sets&#39;: {&#39;type&#39;: &#39;list&#39;, &#39;required&#39;: True, &#39;schema&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;schema&#39;: {&#39;name&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True}, &#39;file&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: False, &#39;schema&#39;: {&#39;path&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True}, &#39;columns&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: True}, &#39;category&#39;: {&#39;type&#39;: &#39;string&#39;}, &#39;actions&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;schema&#39;: {&#39;divide_col&#39;: {&#39;type&#39;: &#39;string&#39;}}}}}, &#39;metadata&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: True}}}}}}}</span>
+            <label class="view-value-button pdoc-button" for="CONFIG_SCHEMA-view-value"></label><span class="default_value">{&#39;phenotype&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: True, &#39;schema&#39;: {&#39;version&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True, &#39;regex&#39;: &#39;^\\d+\\.\\d+\\.\\d+$&#39;}, &#39;omop&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: True, &#39;schema&#39;: {&#39;vocabulary_id&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True}, &#39;vocabulary_name&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True}, &#39;vocabulary_reference&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True, &#39;regex&#39;: &#39;^https?://.*&#39;}}}, &#39;map&#39;: {&#39;type&#39;: &#39;list&#39;, &#39;schema&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;allowed&#39;: [&#39;snomed&#39;, &#39;opcs4&#39;, &#39;read2&#39;, &#39;icd10&#39;, &#39;atc&#39;, &#39;read3&#39;]}}, &#39;concept_sets&#39;: {&#39;type&#39;: &#39;list&#39;, &#39;required&#39;: True, &#39;schema&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;schema&#39;: {&#39;name&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True}, &#39;file&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: False, &#39;schema&#39;: {&#39;path&#39;: {&#39;type&#39;: &#39;string&#39;, &#39;required&#39;: True}, &#39;columns&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: True}, &#39;category&#39;: {&#39;type&#39;: &#39;string&#39;}, &#39;actions&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;schema&#39;: {&#39;divide_col&#39;: {&#39;type&#39;: &#39;string&#39;}}}}}, &#39;metadata&#39;: {&#39;type&#39;: &#39;dict&#39;, &#39;required&#39;: True}}}}}}}</span>
 
         
     </div>
@@ -2085,12 +2085,18 @@
 
             <div class="docstring"><p>Checks on the command line if a user wants to delete a directory</p>
 
-<p>Args:
-    path (Path): path of the directory to be deleted
-    msg (str): message to be displayed to the user</p>
+<h6 id="arguments">Arguments:</h6>
 
-<p>Returns:
-    Boolean: True if deleted</p>
+<ul>
+<li><strong>path (Path):</strong>  path of the directory to be deleted</li>
+<li><strong>msg (str):</strong>  message to be displayed to the user</li>
+</ul>
+
+<h6 id="returns">Returns:</h6>
+
+<blockquote>
+  <p>Boolean: True if deleted</p>
+</blockquote>
 </div>
 
 
@@ -2201,16 +2207,22 @@
 
             <div class="docstring"><p>Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin"</p>
 
-<p>Args:
-    phen_dir (str): local directory path where the upstream repo is to be cloned
-    upstream_url (str): url to the upstream repo
-    upstream_version (str): version in the upstream repo to clone
-    new_origin_url (str, optional): url of the remote repo to set as the new origin. Defaults to None.</p>
+<h6 id="arguments">Arguments:</h6>
+
+<ul>
+<li><strong>phen_dir (str):</strong>  local directory path where the upstream repo is to be cloned</li>
+<li><strong>upstream_url (str):</strong>  url to the upstream repo</li>
+<li><strong>upstream_version (str):</strong>  version in the upstream repo to clone</li>
+<li><strong>new_origin_url (str, optional):</strong>  url of the remote repo to set as the new origin. Defaults to None.</li>
+</ul>
+
+<h6 id="raises">Raises:</h6>
 
-<p>Raises:
-    ValueError: if the specified version is not in the upstream repo
-    ValueError: if the upstream repo is not a valid phenotype repo
-    ValueError: if there's any other problems with Git</p>
+<ul>
+<li><strong>ValueError:</strong>  if the specified version is not in the upstream repo</li>
+<li><strong>ValueError:</strong>  if the upstream repo is not a valid phenotype repo</li>
+<li><strong>ValueError:</strong>  if there's any other problems with Git</li>
+</ul>
 </div>
 
 
@@ -3378,9 +3390,18 @@
 
             <div class="docstring"><p>Extracts clean keys from a DeepDiff dictionary.</p>
 
-<p>:param diff: DeepDiff result dictionary
-:param key_type: The type of change to extract (e.g., "dictionary_item_added", "dictionary_item_removed")
-:return: A set of clean key names</p>
+<h6 id="parameters">Parameters</h6>
+
+<ul>
+<li><strong>diff</strong>:  DeepDiff result dictionary</li>
+<li><strong>key_type</strong>:  The type of change to extract (e.g., "dictionary_item_added", "dictionary_item_removed")</li>
+</ul>
+
+<h6 id="returns">Returns</h6>
+
+<blockquote>
+  <p>A set of clean key names</p>
+</blockquote>
 </div>
 
 
diff --git a/docs/api/search.js b/docs/api/search.js
index c4ef4d4be3d29c8e438f08fe9f6b0e251558a692..511a05d26f22aedd42771f35265cf79c073e8a1b 100644
--- a/docs/api/search.js
+++ b/docs/api/search.js
@@ -1,6 +1,6 @@
 window.pdocSearch = (function(){
 /** elasticlunr - http://weixsong.github.io * Copyright (C) 2017 Oliver Nightingale * Copyright (C) 2017 Wei Song * MIT Licensed */!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. This may cause problems when serialising the index.\n",e)},t.Pipeline.load=function(e){var n=new t.Pipeline;return e.forEach(function(e){var i=t.Pipeline.getRegisteredFunction(e);if(!i)throw new Error("Cannot load un-registered function: "+e);n.add(i)}),n},t.Pipeline.prototype.add=function(){var e=Array.prototype.slice.call(arguments);e.forEach(function(e){t.Pipeline.warnIfFunctionNotRegistered(e),this._queue.push(e)},this)},t.Pipeline.prototype.after=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i+1,0,n)},t.Pipeline.prototype.before=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i,0,n)},t.Pipeline.prototype.remove=function(e){var t=this._queue.indexOf(e);-1!==t&&this._queue.splice(t,1)},t.Pipeline.prototype.run=function(e){for(var t=[],n=e.length,i=this._queue.length,o=0;n>o;o++){for(var r=e[o],s=0;i>s&&(r=this._queue[s](r,o,e),void 0!==r&&null!==r);s++);void 0!==r&&null!==r&&t.push(r)}return t},t.Pipeline.prototype.reset=function(){this._queue=[]},t.Pipeline.prototype.get=function(){return this._queue},t.Pipeline.prototype.toJSON=function(){return this._queue.map(function(e){return t.Pipeline.warnIfFunctionNotRegistered(e),e.label})},t.Index=function(){this._fields=[],this._ref="id",this.pipeline=new t.Pipeline,this.documentStore=new t.DocumentStore,this.index={},this.eventEmitter=new t.EventEmitter,this._idfCache={},this.on("add","remove","update",function(){this._idfCache={}}.bind(this))},t.Index.prototype.on=function(){var e=Array.prototype.slice.call(arguments);return this.eventEmitter.addListener.apply(this.eventEmitter,e)},t.Index.prototype.off=function(e,t){return this.eventEmitter.removeListener(e,t)},t.Index.load=function(e){e.version!==t.version&&t.utils.warn("version mismatch: current "+t.version+" 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u=r[s];u=Math.sqrt(u),this.index[n].addToken(s,{ref:i,tf:u})}},this),n&&this.eventEmitter.emit("add",e,this)}},t.Index.prototype.removeDocByRef=function(e){if(e&&this.documentStore.isDocStored()!==!1&&this.documentStore.hasDoc(e)){var t=this.documentStore.getDoc(e);this.removeDoc(t,!1)}},t.Index.prototype.removeDoc=function(e,n){if(e){var n=void 0===n?!0:n,i=e[this._ref];this.documentStore.hasDoc(i)&&(this.documentStore.removeDoc(i),this._fields.forEach(function(n){var o=this.pipeline.run(t.tokenizer(e[n]));o.forEach(function(e){this.index[n].removeToken(e,i)},this)},this),n&&this.eventEmitter.emit("remove",e,this))}},t.Index.prototype.updateDoc=function(e,t){var t=void 0===t?!0:t;this.removeDocByRef(e[this._ref],!1),this.addDoc(e,!1),t&&this.eventEmitter.emit("update",e,this)},t.Index.prototype.idf=function(e,t){var n="@"+t+"/"+e;if(Object.prototype.hasOwnProperty.call(this._idfCache,n))return this._idfCache[n];var i=this.index[t].getDocFreq(e),o=1+Math.log(this.documentStore.length/(i+1));return this._idfCache[n]=o,o},t.Index.prototype.getFields=function(){return this._fields.slice()},t.Index.prototype.search=function(e,n){if(!e)return[];e="string"==typeof e?{any:e}:JSON.parse(JSON.stringify(e));var i=null;null!=n&&(i=JSON.stringify(n));for(var o=new t.Configuration(i,this.getFields()).get(),r={},s=Object.keys(e),u=0;u<s.length;u++){var a=s[u];r[a]=this.pipeline.run(t.tokenizer(e[a]))}var l={};for(var c in o){var d=r[c]||r.any;if(d){var f=this.fieldSearch(d,c,o),h=o[c].boost;for(var p in f)f[p]=f[p]*h;for(var p in f)p in l?l[p]+=f[p]:l[p]=f[p]}}var v,g=[];for(var p in l)v={ref:p,score:l[p]},this.documentStore.hasDoc(p)&&(v.doc=this.documentStore.getDoc(p)),g.push(v);return g.sort(function(e,t){return t.score-e.score}),g},t.Index.prototype.fieldSearch=function(e,t,n){var i=n[t].bool,o=n[t].expand,r=n[t].boost,s=null,u={};return 0!==r?(e.forEach(function(e){var 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e={ational:"ate",tional:"tion",enci:"ence",anci:"ance",izer:"ize",bli:"ble",alli:"al",entli:"ent",eli:"e",ousli:"ous",ization:"ize",ation:"ate",ator:"ate",alism:"al",iveness:"ive",fulness:"ful",ousness:"ous",aliti:"al",iviti:"ive",biliti:"ble",logi:"log"},t={icate:"ic",ative:"",alize:"al",iciti:"ic",ical:"ic",ful:"",ness:""},n="[^aeiou]",i="[aeiouy]",o=n+"[^aeiouy]*",r=i+"[aeiou]*",s="^("+o+")?"+r+o,u="^("+o+")?"+r+o+"("+r+")?$",a="^("+o+")?"+r+o+r+o,l="^("+o+")?"+i,c=new RegExp(s),d=new RegExp(a),f=new RegExp(u),h=new RegExp(l),p=/^(.+?)(ss|i)es$/,v=/^(.+?)([^s])s$/,g=/^(.+?)eed$/,m=/^(.+?)(ed|ing)$/,y=/.$/,S=/(at|bl|iz)$/,x=new RegExp("([^aeiouylsz])\\1$"),w=new 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0===e)throw new Error("token should not be undefined");return e.replace(/^\W+/,"").replace(/\W+$/,"")},t.Pipeline.registerFunction(t.trimmer,"trimmer"),t.InvertedIndex=function(){this.root={docs:{},df:0}},t.InvertedIndex.load=function(e){var t=new this;return t.root=e.root,t},t.InvertedIndex.prototype.addToken=function(e,t,n){for(var n=n||this.root,i=0;i<=e.length-1;){var o=e[i];o in n||(n[o]={docs:{},df:0}),i+=1,n=n[o]}var r=t.ref;n.docs[r]?n.docs[r]={tf:t.tf}:(n.docs[r]={tf:t.tf},n.df+=1)},t.InvertedIndex.prototype.hasToken=function(e){if(!e)return!1;for(var t=this.root,n=0;n<e.length;n++){if(!t[e[n]])return!1;t=t[e[n]]}return!0},t.InvertedIndex.prototype.getNode=function(e){if(!e)return null;for(var t=this.root,n=0;n<e.length;n++){if(!t[e[n]])return null;t=t[e[n]]}return t},t.InvertedIndex.prototype.getDocs=function(e){var t=this.getNode(e);return null==t?{}:t.docs},t.InvertedIndex.prototype.getTermFrequency=function(e,t){var n=this.getNode(e);return null==n?0:t in n.docs?n.docs[t].tf:0},t.InvertedIndex.prototype.getDocFreq=function(e){var t=this.getNode(e);return null==t?0:t.df},t.InvertedIndex.prototype.removeToken=function(e,t){if(e){var n=this.getNode(e);null!=n&&t in n.docs&&(delete n.docs[t],n.df-=1)}},t.InvertedIndex.prototype.expandToken=function(e,t,n){if(null==e||""==e)return[];var t=t||[];if(void 0==n&&(n=this.getNode(e),null==n))return t;n.df>0&&t.push(e);for(var i in n)"docs"!==i&&"df"!==i&&this.expandToken(e+i,t,n[i]);return t},t.InvertedIndex.prototype.toJSON=function(){return{root:this.root}},t.Configuration=function(e,n){var e=e||"";if(void 0==n||null==n)throw new Error("fields should not be null");this.config={};var i;try{i=JSON.parse(e),this.buildUserConfig(i,n)}catch(o){t.utils.warn("user configuration parse failed, will use default configuration"),this.buildDefaultConfig(n)}},t.Configuration.prototype.buildDefaultConfig=function(e){this.reset(),e.forEach(function(e){this.config[e]={boost:1,bool:"OR",expand:!1}},this)},t.Configuration.prototype.buildUserConfig=function(e,n){var i="OR",o=!1;if(this.reset(),"bool"in e&&(i=e.bool||i),"expand"in e&&(o=e.expand||o),"fields"in e)for(var r in e.fields)if(n.indexOf(r)>-1){var s=e.fields[r],u=o;void 0!=s.expand&&(u=s.expand),this.config[r]={boost:s.boost||0===s.boost?s.boost:1,bool:s.bool||i,expand:u}}else t.utils.warn("field name in user configuration not found in index instance fields");else this.addAllFields2UserConfig(i,o,n)},t.Configuration.prototype.addAllFields2UserConfig=function(e,t,n){n.forEach(function(n){this.config[n]={boost:1,bool:e,expand:t}},this)},t.Configuration.prototype.get=function(){return 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"doc": "<p>Handle the <code>phen map</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_export": {"fullname": "acmc.main.phen_export", "modulename": "acmc.main", "qualname": "phen_export", "kind": "function", "doc": "<p>Handle the <code>phen copy</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_publish": {"fullname": "acmc.main.phen_publish", "modulename": "acmc.main", "qualname": "phen_publish", "kind": "function", "doc": "<p>Handle the <code>phen publish</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_copy": {"fullname": "acmc.main.phen_copy", "modulename": "acmc.main", "qualname": "phen_copy", "kind": "function", "doc": "<p>Handle the <code>phen copy</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_diff": {"fullname": "acmc.main.phen_diff", "modulename": "acmc.main", "qualname": "phen_diff", "kind": "function", "doc": "<p>Handle the <code>phen diff</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.main": {"fullname": "acmc.main.main", "modulename": "acmc.main", "qualname": "main", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop": {"fullname": "acmc.omop", "modulename": "acmc.omop", "kind": "module", "doc": "<h1 id=\"omop-module\">OMOP Module</h1>\n\n<p>This module provides functionality to manage OMOP vocabularies.</p>\n"}, "acmc.omop.logger": {"fullname": "acmc.omop.logger", "modulename": "acmc.omop", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "&lt;Logger acmc_logger (INFO)&gt;"}, "acmc.omop.VOCAB_PATH": {"fullname": "acmc.omop.VOCAB_PATH", "modulename": "acmc.omop", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/omop&#x27;)"}, "acmc.omop.OMOP_CDM_Version": {"fullname": "acmc.omop.OMOP_CDM_Version", "modulename": "acmc.omop", "qualname": "OMOP_CDM_Version", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;54&#x27;"}, "acmc.omop.OMOP_DB_FILENAME": {"fullname": "acmc.omop.OMOP_DB_FILENAME", "modulename": "acmc.omop", "qualname": "OMOP_DB_FILENAME", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;omop_54.sqlite&#x27;"}, "acmc.omop.DB_PATH": {"fullname": "acmc.omop.DB_PATH", "modulename": "acmc.omop", "qualname": "DB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/omop/omop_54.sqlite&#x27;)"}, "acmc.omop.VERSION_FILE": {"fullname": "acmc.omop.VERSION_FILE", "modulename": "acmc.omop", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;omop_version.yaml&#x27;"}, "acmc.omop.VERSION_PATH": {"fullname": "acmc.omop.VERSION_PATH", "modulename": "acmc.omop", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/omop/omop_version.yaml&#x27;)"}, "acmc.omop.EXPORT_FILE": {"fullname": "acmc.omop.EXPORT_FILE", "modulename": "acmc.omop", "qualname": "EXPORT_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;omop_54_export.sqlite&#x27;"}, "acmc.omop.vocabularies": {"fullname": "acmc.omop.vocabularies", "modulename": "acmc.omop", "qualname": "vocabularies", "kind": "variable", "doc": "<p></p>\n", "default_value": "{&#x27;source&#x27;: &#x27;OHDSI Athena&#x27;, &#x27;url&#x27;: &#x27;https://athena.ohdsi.org/vocabulary/list&#x27;, &#x27;cdm_version&#x27;: &#x27;54&#x27;, &#x27;version&#x27;: &#x27;&#x27;, &#x27;vocabularies&#x27;: [{&#x27;id&#x27;: 1, &#x27;name&#x27;: &#x27;SNOMED&#x27;}, {&#x27;id&#x27;: 2, &#x27;name&#x27;: &#x27;ICD9CM&#x27;}, {&#x27;id&#x27;: 17, &#x27;name&#x27;: &#x27;Readv2&#x27;}, {&#x27;id&#x27;: 21, &#x27;name&#x27;: &#x27;ATC&#x27;}, {&#x27;id&#x27;: 55, &#x27;name&#x27;: &#x27;OPCS4&#x27;}, {&#x27;id&#x27;: 57, &#x27;name&#x27;: &#x27;HES Specialty&#x27;}, {&#x27;id&#x27;: 70, &#x27;name&#x27;: &#x27;ICD10CM&#x27;}, {&#x27;id&#x27;: 75, &#x27;name&#x27;: &#x27;dm+d&#x27;}, {&#x27;id&#x27;: 144, &#x27;name&#x27;: &#x27;UK Biobank&#x27;}, {&#x27;id&#x27;: 154, &#x27;name&#x27;: &#x27;NHS Ethnic Category&#x27;}, {&#x27;id&#x27;: 155, &#x27;name&#x27;: &#x27;NHS Place of Service&#x27;}], &#x27;tables&#x27;: []}"}, "acmc.omop.omop_vocab_types": {"fullname": "acmc.omop.omop_vocab_types", "modulename": "acmc.omop", "qualname": "omop_vocab_types", "kind": "variable", "doc": "<p></p>\n", "default_value": "{&#x27;read2&#x27;: &#x27;Read&#x27;, &#x27;read3&#x27;: None, &#x27;icd10&#x27;: &#x27;ICD10CM&#x27;, &#x27;snomed&#x27;: &#x27;SNOMED&#x27;, &#x27;opcs4&#x27;: &#x27;OPCS4&#x27;, &#x27;atc&#x27;: &#x27;ATC&#x27;, &#x27;med&#x27;: None, &#x27;cprd&#x27;: None}"}, "acmc.omop.install": {"fullname": "acmc.omop.install", "modulename": "acmc.omop", "qualname": "install", "kind": "function", "doc": "<p>Installs the OMOP release csv files in a file-based sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">omop_zip_file</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.write_version_file": {"fullname": "acmc.omop.write_version_file", "modulename": "acmc.omop", "qualname": "write_version_file", "kind": "function", "doc": "<p>Writes the OMOP vocaburaries and version to a file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.clear": {"fullname": "acmc.omop.clear", "modulename": "acmc.omop", "qualname": "clear", "kind": "function", "doc": "<p>Clears the OMOP sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.delete": {"fullname": "acmc.omop.delete", "modulename": "acmc.omop", "qualname": "delete", "kind": "function", "doc": "<p>Deletes the OMOP sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.table_exists": {"fullname": "acmc.omop.table_exists", "modulename": "acmc.omop", "qualname": "table_exists", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">table_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.vocab_exists": {"fullname": "acmc.omop.vocab_exists", "modulename": "acmc.omop", "qualname": "vocab_exists", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">vocab_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.concept_set_exist": {"fullname": "acmc.omop.concept_set_exist", "modulename": "acmc.omop", "qualname": "concept_set_exist", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">concept_set_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.export": {"fullname": "acmc.omop.export", "modulename": "acmc.omop", "qualname": "export", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">export_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">omop_metadata</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.parse": {"fullname": "acmc.parse", "modulename": "acmc.parse", "kind": "module", "doc": "<p></p>\n"}, "acmc.parse.logger": {"fullname": "acmc.parse.logger", "modulename": "acmc.parse", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "&lt;Logger acmc_logger (INFO)&gt;"}, "acmc.parse.SUPPORTED_CODE_TYPES": {"fullname": "acmc.parse.SUPPORTED_CODE_TYPES", "modulename": "acmc.parse", "qualname": "SUPPORTED_CODE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "{&#x27;read2&#x27;, &#x27;icd10&#x27;, &#x27;atc&#x27;, &#x27;snomed&#x27;, &#x27;read3&#x27;, &#x27;opcs4&#x27;}"}, "acmc.parse.CodesError": {"fullname": "acmc.parse.CodesError", "modulename": "acmc.parse", "qualname": "CodesError", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodesError.__init__": {"fullname": "acmc.parse.CodesError.__init__", "modulename": "acmc.parse", "qualname": "CodesError.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">mask</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">code_type</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.InvalidCodesException": {"fullname": "acmc.parse.InvalidCodesException", "modulename": "acmc.parse", "qualname": "InvalidCodesException", "kind": "class", "doc": "<p>Custom exception class raised when invalid codes are found that cannot be resolved by processing</p>\n", "bases": "builtins.Exception"}, "acmc.parse.InvalidCodesException.__init__": {"fullname": "acmc.parse.InvalidCodesException.__init__", "modulename": "acmc.parse", "qualname": "InvalidCodesException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">error</span></span>)</span>"}, "acmc.parse.InvalidCodesException.error": {"fullname": "acmc.parse.InvalidCodesException.error", "modulename": "acmc.parse", "qualname": "InvalidCodesException.error", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Proto": {"fullname": "acmc.parse.Proto", "modulename": "acmc.parse", "qualname": "Proto", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n"}, "acmc.parse.Proto.__init__": {"fullname": "acmc.parse.Proto.__init__", "modulename": "acmc.parse", "qualname": "Proto.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">name</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">trud_codes_path</span><span class=\"p\">:</span> <span class=\"n\">Optional</span><span class=\"p\">[</span><span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span><span class=\"p\">]</span> <span class=\"o\">=</span> <span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.Proto.checks": {"fullname": "acmc.parse.Proto.checks", "modulename": "acmc.parse", "qualname": "Proto.checks", "kind": "variable", "doc": "<p></p>\n", "annotation": ": list[tuple[str, typing.Callable[[pandas.core.frame.DataFrame], pandas.core.series.Series], typing.Callable[[pandas.core.frame.DataFrame, pathlib.Path], pandas.core.frame.DataFrame]]]"}, "acmc.parse.Proto.name": {"fullname": "acmc.parse.Proto.name", "modulename": "acmc.parse", "qualname": "Proto.name", "kind": "variable", "doc": "<p></p>\n", "annotation": ": str"}, "acmc.parse.Proto.raise_exception": {"fullname": "acmc.parse.Proto.raise_exception", "modulename": "acmc.parse", "qualname": "Proto.raise_exception", "kind": "function", "doc": "<p>Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">ex</span><span class=\"p\">:</span> <span class=\"ne\">Exception</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Proto.in_database": {"fullname": "acmc.parse.Proto.in_database", "modulename": "acmc.parse", "qualname": "Proto.in_database", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">db</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">col</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.process": {"fullname": "acmc.parse.Proto.process", "modulename": "acmc.parse", "qualname": "Proto.process", "kind": "function", "doc": "<p>identify issues that do not pass and fix them with define/d process</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.verify": {"fullname": "acmc.parse.Proto.verify", "modulename": "acmc.parse", "qualname": "Proto.verify", "kind": "function", "doc": "<p>verify codes in codes file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Read2": {"fullname": "acmc.parse.Read2", "modulename": "acmc.parse", "qualname": "Read2", "kind": "class", "doc": "<p>This Read2 class extends Proto, adding custom validation checks for a dataset of \"Read2\" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary.</p>\n", "bases": "Proto"}, "acmc.parse.Read2.checks": {"fullname": "acmc.parse.Read2.checks", "modulename": "acmc.parse", "qualname": "Read2.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Read3": {"fullname": "acmc.parse.Read3", "modulename": "acmc.parse", "qualname": "Read3", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Read3.checks": {"fullname": "acmc.parse.Read3.checks", "modulename": "acmc.parse", "qualname": "Read3.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Icd10": {"fullname": "acmc.parse.Icd10", "modulename": "acmc.parse", "qualname": "Icd10", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Icd10.checks": {"fullname": "acmc.parse.Icd10.checks", "modulename": "acmc.parse", "qualname": "Icd10.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Snomed": {"fullname": "acmc.parse.Snomed", "modulename": "acmc.parse", "qualname": "Snomed", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Snomed.checks": {"fullname": "acmc.parse.Snomed.checks", "modulename": "acmc.parse", "qualname": "Snomed.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Opcs4": {"fullname": "acmc.parse.Opcs4", "modulename": "acmc.parse", "qualname": "Opcs4", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Opcs4.checks": {"fullname": "acmc.parse.Opcs4.checks", "modulename": "acmc.parse", "qualname": "Opcs4.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Atc": {"fullname": "acmc.parse.Atc", "modulename": "acmc.parse", "qualname": "Atc", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Atc.checks": {"fullname": "acmc.parse.Atc.checks", "modulename": "acmc.parse", "qualname": "Atc.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Med": {"fullname": "acmc.parse.Med", "modulename": "acmc.parse", "qualname": "Med", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Med.checks": {"fullname": "acmc.parse.Med.checks", "modulename": "acmc.parse", "qualname": "Med.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Cprd": {"fullname": "acmc.parse.Cprd", "modulename": "acmc.parse", "qualname": "Cprd", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Cprd.checks": {"fullname": "acmc.parse.Cprd.checks", "modulename": "acmc.parse", "qualname": "Cprd.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.CodeTypeParser": {"fullname": "acmc.parse.CodeTypeParser", "modulename": "acmc.parse", "qualname": "CodeTypeParser", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodeTypeParser.__init__": {"fullname": "acmc.parse.CodeTypeParser.__init__", "modulename": "acmc.parse", "qualname": "CodeTypeParser.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">trud_processed_dir</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span> <span class=\"o\">=</span> <span class=\"n\">PosixPath</span><span class=\"p\">(</span><span class=\"s1\">&#39;vocab/trud/processed&#39;</span><span class=\"p\">)</span></span>)</span>"}, "acmc.parse.CodeTypeParser.code_types": {"fullname": "acmc.parse.CodeTypeParser.code_types", "modulename": "acmc.parse", "qualname": "CodeTypeParser.code_types", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen": {"fullname": "acmc.phen", "modulename": "acmc.phen", "kind": "module", "doc": "<h1 id=\"phenotype-module\">Phenotype Module</h1>\n\n<p>This module provides functionality for managing phenotypes.</p>\n"}, "acmc.phen.logger": {"fullname": "acmc.phen.logger", "modulename": "acmc.phen", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "&lt;Logger acmc_logger (INFO)&gt;"}, "acmc.phen.PHEN_DIR": {"fullname": "acmc.phen.PHEN_DIR", "modulename": "acmc.phen", "qualname": "PHEN_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;phen&#x27;"}, "acmc.phen.DEFAULT_PHEN_PATH": {"fullname": "acmc.phen.DEFAULT_PHEN_PATH", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;workspace/phen&#x27;)"}, "acmc.phen.CONCEPTS_DIR": {"fullname": "acmc.phen.CONCEPTS_DIR", "modulename": "acmc.phen", "qualname": "CONCEPTS_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;concepts&#x27;"}, "acmc.phen.MAP_DIR": {"fullname": "acmc.phen.MAP_DIR", "modulename": "acmc.phen", "qualname": "MAP_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;map&#x27;"}, "acmc.phen.CONCEPT_SET_DIR": {"fullname": "acmc.phen.CONCEPT_SET_DIR", "modulename": "acmc.phen", "qualname": "CONCEPT_SET_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;concept-sets&#x27;"}, "acmc.phen.CSV_PATH": {"fullname": "acmc.phen.CSV_PATH", "modulename": "acmc.phen", "qualname": "CSV_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;concept-sets/csv&#x27;)"}, "acmc.phen.OMOP_PATH": {"fullname": "acmc.phen.OMOP_PATH", "modulename": "acmc.phen", "qualname": "OMOP_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;concept-sets/omop&#x27;)"}, "acmc.phen.DEFAULT_PHEN_DIR_LIST": {"fullname": "acmc.phen.DEFAULT_PHEN_DIR_LIST", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_DIR_LIST", "kind": "variable", "doc": "<p></p>\n", "default_value": "[&#x27;concepts&#x27;, &#x27;map&#x27;, &#x27;concept-sets&#x27;]"}, "acmc.phen.CONFIG_FILE": {"fullname": "acmc.phen.CONFIG_FILE", "modulename": "acmc.phen", "qualname": "CONFIG_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;config.yaml&#x27;"}, "acmc.phen.VOCAB_VERSION_FILE": {"fullname": "acmc.phen.VOCAB_VERSION_FILE", "modulename": "acmc.phen", "qualname": "VOCAB_VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;vocab_version.yaml&#x27;"}, "acmc.phen.SEMANTIC_VERSION_TYPES": {"fullname": "acmc.phen.SEMANTIC_VERSION_TYPES", "modulename": "acmc.phen", "qualname": "SEMANTIC_VERSION_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "[&#x27;major&#x27;, &#x27;minor&#x27;, &#x27;patch&#x27;]"}, "acmc.phen.DEFAULT_VERSION_INC": {"fullname": "acmc.phen.DEFAULT_VERSION_INC", "modulename": "acmc.phen", "qualname": "DEFAULT_VERSION_INC", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;patch&#x27;"}, "acmc.phen.DEFAULT_GIT_BRANCH": {"fullname": "acmc.phen.DEFAULT_GIT_BRANCH", "modulename": "acmc.phen", "qualname": "DEFAULT_GIT_BRANCH", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;main&#x27;"}, "acmc.phen.SPLIT_COL_ACTION": {"fullname": "acmc.phen.SPLIT_COL_ACTION", "modulename": "acmc.phen", "qualname": "SPLIT_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;split_col&#x27;"}, "acmc.phen.CODES_COL_ACTION": {"fullname": "acmc.phen.CODES_COL_ACTION", "modulename": "acmc.phen", "qualname": "CODES_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;codes_col&#x27;"}, "acmc.phen.DIVIDE_COL_ACTION": {"fullname": "acmc.phen.DIVIDE_COL_ACTION", "modulename": "acmc.phen", "qualname": "DIVIDE_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;divide_col&#x27;"}, "acmc.phen.COL_ACTIONS": {"fullname": "acmc.phen.COL_ACTIONS", "modulename": "acmc.phen", "qualname": "COL_ACTIONS", "kind": "variable", "doc": "<p></p>\n", "default_value": "[&#x27;split_col&#x27;, &#x27;codes_col&#x27;, &#x27;divide_col&#x27;]"}, "acmc.phen.CODE_FILE_TYPES": {"fullname": "acmc.phen.CODE_FILE_TYPES", "modulename": "acmc.phen", "qualname": "CODE_FILE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "[&#x27;.xlsx&#x27;, &#x27;.xls&#x27;, &#x27;.csv&#x27;]"}, "acmc.phen.SOURCE_COL_SUFFIX": {"fullname": "acmc.phen.SOURCE_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "SOURCE_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;_acmc_source&#x27;"}, "acmc.phen.TARGET_COL_SUFFIX": {"fullname": "acmc.phen.TARGET_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "TARGET_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;_acmc_target&#x27;"}, "acmc.phen.CONFIG_SCHEMA": {"fullname": "acmc.phen.CONFIG_SCHEMA", "modulename": "acmc.phen", "qualname": "CONFIG_SCHEMA", "kind": "variable", "doc": "<p></p>\n", "default_value": "{&#x27;phenotype&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: True, &#x27;schema&#x27;: {&#x27;version&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True, &#x27;regex&#x27;: &#x27;^\\\\d+\\\\.\\\\d+\\\\.\\\\d+$&#x27;}, &#x27;omop&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: True, &#x27;schema&#x27;: {&#x27;vocabulary_id&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True}, &#x27;vocabulary_name&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True}, &#x27;vocabulary_reference&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True, &#x27;regex&#x27;: &#x27;^https?://.*&#x27;}}}, &#x27;map&#x27;: {&#x27;type&#x27;: &#x27;list&#x27;, &#x27;schema&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;allowed&#x27;: [&#x27;read2&#x27;, &#x27;icd10&#x27;, &#x27;atc&#x27;, &#x27;snomed&#x27;, &#x27;read3&#x27;, &#x27;opcs4&#x27;]}}, &#x27;concept_sets&#x27;: {&#x27;type&#x27;: &#x27;list&#x27;, &#x27;required&#x27;: True, &#x27;schema&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;schema&#x27;: {&#x27;name&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True}, &#x27;file&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: False, &#x27;schema&#x27;: {&#x27;path&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True}, &#x27;columns&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: True}, &#x27;category&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;}, &#x27;actions&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;schema&#x27;: {&#x27;divide_col&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;}}}}}, &#x27;metadata&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: True}}}}}}}"}, "acmc.phen.PhenValidationException": {"fullname": "acmc.phen.PhenValidationException", "modulename": "acmc.phen", "qualname": "PhenValidationException", "kind": "class", "doc": "<p>Custom exception class raised when validation errors in phenotype configuration file</p>\n", "bases": "builtins.Exception"}, "acmc.phen.PhenValidationException.__init__": {"fullname": "acmc.phen.PhenValidationException.__init__", "modulename": "acmc.phen", "qualname": "PhenValidationException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">validation_errors</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.phen.PhenValidationException.validation_errors": {"fullname": "acmc.phen.PhenValidationException.validation_errors", "modulename": "acmc.phen", "qualname": "PhenValidationException.validation_errors", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen.construct_git_url": {"fullname": "acmc.phen.construct_git_url", "modulename": "acmc.phen", "qualname": "construct_git_url", "kind": "function", "doc": "<p>Constructs a git url for github or gitlab including a PAT token environment variable</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.create_empty_git_dir": {"fullname": "acmc.phen.create_empty_git_dir", "modulename": "acmc.phen", "qualname": "create_empty_git_dir", "kind": "function", "doc": "<p>Creates a directory with a .gitkeep file so that it's tracked in git</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.check_delete_dir": {"fullname": "acmc.phen.check_delete_dir", "modulename": "acmc.phen", "qualname": "check_delete_dir", "kind": "function", "doc": "<p>Checks on the command line if a user wants to delete a directory</p>\n\n<p>Args:\n    path (Path): path of the directory to be deleted\n    msg (str): message to be displayed to the user</p>\n\n<p>Returns:\n    Boolean: True if deleted</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.fork": {"fullname": "acmc.phen.fork", "modulename": "acmc.phen", "qualname": "fork", "kind": "function", "doc": "<p>Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin\"</p>\n\n<p>Args:\n    phen_dir (str): local directory path where the upstream repo is to be cloned\n    upstream_url (str): url to the upstream repo\n    upstream_version (str): version in the upstream repo to clone\n    new_origin_url (str, optional): url of the remote repo to set as the new origin. Defaults to None.</p>\n\n<p>Raises:\n    ValueError: if the specified version is not in the upstream repo\n    ValueError: if the upstream repo is not a valid phenotype repo\n    ValueError: if there's any other problems with Git</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">new_origin_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.init": {"fullname": "acmc.phen.init", "modulename": "acmc.phen", "qualname": "init", "kind": "function", "doc": "<p>Initial phenotype directory as git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.validate": {"fullname": "acmc.phen.validate", "modulename": "acmc.phen", "qualname": "validate", "kind": "function", "doc": "<p>Validates the phenotype directory is a git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.read_table_file": {"fullname": "acmc.phen.read_table_file", "modulename": "acmc.phen", "qualname": "read_table_file", "kind": "function", "doc": "<p>Load Code List File</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">excel_sheet</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">&#39;&#39;</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.process_actions": {"fullname": "acmc.phen.process_actions", "modulename": "acmc.phen", "qualname": "process_actions", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.preprocess_source_concepts": {"fullname": "acmc.phen.preprocess_source_concepts", "modulename": "acmc.phen", "qualname": "preprocess_source_concepts", "kind": "function", "doc": "<p>Parses each column individually - Order and length will not be preserved!</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">code_file_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.get_code_type_from_col_name": {"fullname": "acmc.phen.get_code_type_from_col_name", "modulename": "acmc.phen", "qualname": "get_code_type_from_col_name", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">col_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.translate_codes": {"fullname": "acmc.phen.translate_codes", "modulename": "acmc.phen", "qualname": "translate_codes", "kind": "function", "doc": "<p>Translates each source code type the source coding list into a target type and returns all conversions as a concept set</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">source_df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">concept_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.sql_row_exist": {"fullname": "acmc.phen.sql_row_exist", "modulename": "acmc.phen", "qualname": "sql_row_exist", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">conn</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Connection</span>, </span><span class=\"param\"><span class=\"n\">table</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">column</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">value</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.write_code_errors": {"fullname": "acmc.phen.write_code_errors", "modulename": "acmc.phen", "qualname": "write_code_errors", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">code_errors</span><span class=\"p\">:</span> <span class=\"nb\">list</span>, </span><span class=\"param\"><span class=\"n\">code_errors_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.write_vocab_version": {"fullname": "acmc.phen.write_vocab_version", "modulename": "acmc.phen", "qualname": "write_vocab_version", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map": {"fullname": "acmc.phen.map", "modulename": "acmc.phen", "qualname": "map", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map_target_code_type": {"fullname": "acmc.phen.map_target_code_type", "modulename": "acmc.phen", "qualname": "map_target_code_type", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">phenotype</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.generate_version_tag": {"fullname": "acmc.phen.generate_version_tag", "modulename": "acmc.phen", "qualname": "generate_version_tag", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">repo</span><span class=\"p\">:</span> <span class=\"n\">git</span><span class=\"o\">.</span><span class=\"n\">repo</span><span class=\"o\">.</span><span class=\"n\">base</span><span class=\"o\">.</span><span class=\"n\">Repo</span>,</span><span class=\"param\">\t<span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">&#39;patch&#39;</span>,</span><span class=\"param\">\t<span class=\"n\">use_v_prefix</span><span class=\"p\">:</span> <span class=\"nb\">bool</span> <span class=\"o\">=</span> <span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.publish": {"fullname": "acmc.phen.publish", "modulename": "acmc.phen", "qualname": "publish", "kind": "function", "doc": "<p>Publishes updates to the phenotype by commiting all changes to the repo directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">&#39;patch&#39;</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.export": {"fullname": "acmc.phen.export", "modulename": "acmc.phen", "qualname": "export", "kind": "function", "doc": "<p>Exports a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.copy": {"fullname": "acmc.phen.copy", "modulename": "acmc.phen", "qualname": "copy", "kind": "function", "doc": "<p>Copys a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.extract_concepts": {"fullname": "acmc.phen.extract_concepts", "modulename": "acmc.phen", "qualname": "extract_concepts", "kind": "function", "doc": "<p>Extracts concepts as {name: file_path} dictionary and a name set.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">config_data</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"nb\">dict</span><span class=\"p\">,</span> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"nb\">str</span><span class=\"p\">]]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.extract_clean_deepdiff_keys": {"fullname": "acmc.phen.extract_clean_deepdiff_keys", "modulename": "acmc.phen", "qualname": "extract_clean_deepdiff_keys", "kind": "function", "doc": "<p>Extracts clean keys from a DeepDiff dictionary.</p>\n\n<p>:param diff: DeepDiff result dictionary\n:param key_type: The type of change to extract (e.g., \"dictionary_item_added\", \"dictionary_item_removed\")\n:return: A set of clean key names</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">diff</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">key_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"n\">Any</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_config": {"fullname": "acmc.phen.diff_config", "modulename": "acmc.phen", "qualname": "diff_config", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">new_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_map_files": {"fullname": "acmc.phen.diff_map_files", "modulename": "acmc.phen", "qualname": "diff_map_files", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">new_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_phen": {"fullname": "acmc.phen.diff_phen", "modulename": "acmc.phen", "qualname": "diff_phen", "kind": "function", "doc": "<p>Compare the differences between two versions of a phenotype</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">new_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">new_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">old_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">report_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.diff": {"fullname": "acmc.phen.diff", "modulename": "acmc.phen", "qualname": "diff", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud": {"fullname": "acmc.trud", "modulename": "acmc.trud", "kind": "module", "doc": "<p></p>\n"}, "acmc.trud.logger": {"fullname": "acmc.trud.logger", "modulename": "acmc.trud", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "&lt;Logger acmc_logger (INFO)&gt;"}, "acmc.trud.FQDN": {"fullname": "acmc.trud.FQDN", "modulename": "acmc.trud", "qualname": "FQDN", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;isd.digital.nhs.uk&#x27;"}, "acmc.trud.VOCAB_PATH": {"fullname": "acmc.trud.VOCAB_PATH", "modulename": "acmc.trud", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/trud&#x27;)"}, "acmc.trud.VERSION_FILE": {"fullname": "acmc.trud.VERSION_FILE", "modulename": "acmc.trud", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;trud_version.yaml&#x27;"}, "acmc.trud.VERSION_PATH": {"fullname": "acmc.trud.VERSION_PATH", "modulename": "acmc.trud", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/trud/trud_version.yaml&#x27;)"}, "acmc.trud.DOWNLOADS_PATH": {"fullname": "acmc.trud.DOWNLOADS_PATH", "modulename": "acmc.trud", "qualname": "DOWNLOADS_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/trud/downloads&#x27;)"}, "acmc.trud.PROCESSED_PATH": {"fullname": "acmc.trud.PROCESSED_PATH", "modulename": "acmc.trud", "qualname": "PROCESSED_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/trud/processed&#x27;)"}, "acmc.trud.get_releases": {"fullname": "acmc.trud.get_releases", "modulename": "acmc.trud", "qualname": "get_releases", "kind": "function", "doc": "<p>Retrieve release information for an item from the TRUD API.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">API_KEY</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">latest</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">list</span>:</span></span>", "funcdef": "def"}, "acmc.trud.download_release_file": {"fullname": "acmc.trud.download_release_file", "modulename": "acmc.trud", "qualname": "download_release_file", "kind": "function", "doc": "<p>Download specified file type for a given release of an item.</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release_ordinal</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">file_json_prefix</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.trud.validate_download_hash": {"fullname": "acmc.trud.validate_download_hash", "modulename": "acmc.trud", "qualname": "validate_download_hash", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">item_hash</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.unzip_download": {"fullname": "acmc.trud.unzip_download", "modulename": "acmc.trud", "qualname": "unzip_download", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_icd10": {"fullname": "acmc.trud.extract_icd10", "modulename": "acmc.trud", "qualname": "extract_icd10", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_opsc4": {"fullname": "acmc.trud.extract_opsc4", "modulename": "acmc.trud", "qualname": "extract_opsc4", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_data_migrations": {"fullname": "acmc.trud.extract_nhs_data_migrations", "modulename": "acmc.trud", "qualname": "extract_nhs_data_migrations", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_read_browser": {"fullname": "acmc.trud.extract_nhs_read_browser", "modulename": "acmc.trud", "qualname": "extract_nhs_read_browser", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.create_map_directories": {"fullname": "acmc.trud.create_map_directories", "modulename": "acmc.trud", "qualname": "create_map_directories", "kind": "function", "doc": "<p>Create map directories.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.install": {"fullname": "acmc.trud.install", "modulename": "acmc.trud", "qualname": "install", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.util": {"fullname": "acmc.util", "modulename": "acmc.util", "kind": "module", "doc": "<p></p>\n"}, "acmc.util.QuotedDumper": {"fullname": "acmc.util.QuotedDumper", "modulename": "acmc.util", "qualname": "QuotedDumper", "kind": "class", "doc": "<p></p>\n", "bases": "yaml.dumper.Dumper"}, "acmc.util.QuotedDumper.increase_indent": {"fullname": "acmc.util.QuotedDumper.increase_indent", "modulename": "acmc.util", "qualname": "QuotedDumper.increase_indent", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">flow</span><span class=\"o\">=</span><span class=\"kc\">False</span>, </span><span class=\"param\"><span class=\"n\">indentless</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}}, "docInfo": {"acmc": {"qualname": 0, "fullname": 1, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config": {"qualname": 0, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config.DEFAULT_LOG_FILE": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config.setup_logger": {"qualname": 2, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 24, "bases": 0, "doc": 14}, "acmc.logging_config.set_log_level": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 17, "bases": 0, "doc": 10}, "acmc.main": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.trud_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_clear": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_delete": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_init": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_fork": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_validate": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_map": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_export": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_publish": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_copy": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_diff": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.main": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 7, "bases": 0, "doc": 3}, "acmc.omop": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 15}, "acmc.omop.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VOCAB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_CDM_Version": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_DB_FILENAME": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.DB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VERSION_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VERSION_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.EXPORT_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.vocabularies": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 202, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.omop_vocab_types": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 51, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.install": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 28, "bases": 0, "doc": 14}, "acmc.omop.write_version_file": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 16, "bases": 0, "doc": 11}, "acmc.omop.clear": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 7}, "acmc.omop.delete": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 7}, "acmc.omop.table_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 3}, "acmc.omop.vocab_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 3}, "acmc.omop.concept_set_exist": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 36, "bases": 0, "doc": 3}, "acmc.omop.export": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 66, "bases": 0, "doc": 3}, "acmc.parse": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.SUPPORTED_CODE_TYPES": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 20, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.CodesError": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 17}, "acmc.parse.CodesError.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 51, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 2, "doc": 17}, "acmc.parse.InvalidCodesException.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 9, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException.error": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 59}, "acmc.parse.Proto.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 44, "bases": 0, "doc": 3}, "acmc.parse.Proto.checks": {"qualname": 2, "fullname": 4, "annotation": 22, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto.name": {"qualname": 2, "fullname": 4, "annotation": 2, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto.raise_exception": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 36}, "acmc.parse.Proto.in_database": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 93, "bases": 0, "doc": 3}, "acmc.parse.Proto.process": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 85, "bases": 0, "doc": 14}, "acmc.parse.Proto.verify": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 52, "bases": 0, "doc": 7}, "acmc.parse.Read2": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 40}, "acmc.parse.Read2.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Read3": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Read3.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Icd10": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Icd10.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Snomed": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Snomed.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Opcs4": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Opcs4.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Atc": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Atc.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Med": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Med.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Cprd": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Cprd.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.CodeTypeParser": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 17}, "acmc.parse.CodeTypeParser.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 40, "bases": 0, "doc": 3}, "acmc.parse.CodeTypeParser.code_types": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 14}, "acmc.phen.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.PHEN_DIR": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.DEFAULT_PHEN_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.CONCEPTS_DIR": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.MAP_DIR": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.CONCEPT_SET_DIR": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.CSV_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.OMOP_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.DEFAULT_PHEN_DIR_LIST": {"qualname": 4, "fullname": 6, "annotation": 0, "default_value": 12, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.CONFIG_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.VOCAB_VERSION_FILE": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.SEMANTIC_VERSION_TYPES": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 11, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.DEFAULT_VERSION_INC": {"qualname": 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class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_diff": {"fullname": "acmc.main.phen_diff", "modulename": "acmc.main", "qualname": "phen_diff", "kind": "function", "doc": "<p>Handle the <code>phen diff</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.main": {"fullname": "acmc.main.main", "modulename": "acmc.main", "qualname": "main", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop": {"fullname": "acmc.omop", "modulename": "acmc.omop", "kind": "module", "doc": "<h1 id=\"omop-module\">omop module</h1>\n\n<p>This module provides functionality to manage OMOP vocabularies.</p>\n"}, "acmc.omop.logger": {"fullname": "acmc.omop.logger", "modulename": "acmc.omop", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "&lt;Logger acmc_logger (INFO)&gt;"}, "acmc.omop.VOCAB_PATH": {"fullname": "acmc.omop.VOCAB_PATH", "modulename": "acmc.omop", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/omop&#x27;)"}, "acmc.omop.OMOP_CDM_Version": {"fullname": "acmc.omop.OMOP_CDM_Version", "modulename": "acmc.omop", "qualname": "OMOP_CDM_Version", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;54&#x27;"}, "acmc.omop.OMOP_DB_FILENAME": {"fullname": "acmc.omop.OMOP_DB_FILENAME", "modulename": "acmc.omop", "qualname": "OMOP_DB_FILENAME", "kind": "variable", "doc": "<p></p>\n", 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Service&#x27;}], &#x27;tables&#x27;: []}"}, "acmc.omop.omop_vocab_types": {"fullname": "acmc.omop.omop_vocab_types", "modulename": "acmc.omop", "qualname": "omop_vocab_types", "kind": "variable", "doc": "<p></p>\n", "default_value": "{&#x27;read2&#x27;: &#x27;Read&#x27;, &#x27;read3&#x27;: None, &#x27;icd10&#x27;: &#x27;ICD10CM&#x27;, &#x27;snomed&#x27;: &#x27;SNOMED&#x27;, &#x27;opcs4&#x27;: &#x27;OPCS4&#x27;, &#x27;atc&#x27;: &#x27;ATC&#x27;, &#x27;med&#x27;: None, &#x27;cprd&#x27;: None}"}, "acmc.omop.install": {"fullname": "acmc.omop.install", "modulename": "acmc.omop", "qualname": "install", "kind": "function", "doc": "<p>\"Installs the OMOP release csv files in a file-based sql database</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>omop_zip_file (str):</strong>  vocabularies zip file distributed by OHDSI Athena</li>\n<li><strong>version (str):</strong>  version of the vocabularies distributed by OHDSI Athena</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>ValueError:</strong>  if the zip file does not exist</li>\n<li><strong>ValueError:</strong>  if the file is not a zip file</li>\n<li><strong>Exception:</strong>  if error reading omop csv files</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">omop_zip_file</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.write_version_file": {"fullname": "acmc.omop.write_version_file", "modulename": "acmc.omop", "qualname": "write_version_file", "kind": "function", "doc": "<p>Writes the OMOP vocaburaries and version to a file</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>version (str):</strong>  version of the vocabularies distributed by OHDSI Athena</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.clear": {"fullname": "acmc.omop.clear", "modulename": "acmc.omop", "qualname": "clear", "kind": "function", "doc": "<p>Clears the OMOP sql database</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>db_path (Path):</strong>  the path to the omop sqllite database</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>FileNotFoundError:</strong>  if the omop sqllite database does not exist</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.delete": {"fullname": "acmc.omop.delete", "modulename": "acmc.omop", "qualname": "delete", "kind": "function", "doc": "<p>Deletes the OMOP sql database</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>db_path (Path):</strong>  the path to the omop sqllite database</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>FileNotFoundError:</strong>  if the omop sqllite database does not exist</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.table_exists": {"fullname": "acmc.omop.table_exists", "modulename": "acmc.omop", "qualname": "table_exists", "kind": "function", "doc": "<p>Query to check if the table exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong>  a sqllite database cursor</li>\n<li><strong>table_name (str):</strong>  the table name to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n  <p>bool: true if table exists</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">table_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.vocab_exists": {"fullname": "acmc.omop.vocab_exists", "modulename": "acmc.omop", "qualname": "vocab_exists", "kind": "function", "doc": "<p>Query to check if the vocabulary exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong>  a sqllite database cursor</li>\n<li><strong>vocab_id (str):</strong>  the vocabulary id to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n  <p>bool: true if vocabulary id exists</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">vocab_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.concept_set_exist": {"fullname": "acmc.omop.concept_set_exist", "modulename": "acmc.omop", "qualname": "concept_set_exist", "kind": "function", "doc": "<p>Query to check if the concept set exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong>  a sqllite database cursor</li>\n<li><strong>concept_set_name (str):</strong>  the concept set name to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n  <p>bool: true if concept set exists</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">concept_set_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.export": {"fullname": "acmc.omop.export", "modulename": "acmc.omop", "qualname": "export", "kind": "function", "doc": "<p>Export concept sets to omop database in csv format</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>map_path (Path):</strong>  path to the acmc map directory containing concept sets in csv format</li>\n<li><strong>export_path (Path):</strong>  path to the directory where the omop database csv files are to be written</li>\n<li><strong>version (str):</strong>  phenotype version for omop vocabulary version</li>\n<li><strong>omop_metadata (dict):</strong>  phenotype omop metadata for omop vocabulary metadata </li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n  <p>Path: path to the exported sqllite database</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">export_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">omop_metadata</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.parse": {"fullname": "acmc.parse", "modulename": "acmc.parse", "kind": "module", "doc": "<p></p>\n"}, "acmc.parse.logger": {"fullname": "acmc.parse.logger", "modulename": "acmc.parse", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "&lt;Logger acmc_logger (INFO)&gt;"}, "acmc.parse.SUPPORTED_CODE_TYPES": {"fullname": "acmc.parse.SUPPORTED_CODE_TYPES", "modulename": "acmc.parse", "qualname": "SUPPORTED_CODE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "{&#x27;snomed&#x27;, &#x27;opcs4&#x27;, &#x27;read2&#x27;, &#x27;icd10&#x27;, &#x27;atc&#x27;, &#x27;read3&#x27;}"}, "acmc.parse.CodesError": {"fullname": "acmc.parse.CodesError", "modulename": "acmc.parse", "qualname": "CodesError", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodesError.__init__": {"fullname": "acmc.parse.CodesError.__init__", "modulename": "acmc.parse", "qualname": "CodesError.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">mask</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">code_type</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.InvalidCodesException": {"fullname": "acmc.parse.InvalidCodesException", "modulename": "acmc.parse", "qualname": "InvalidCodesException", "kind": "class", "doc": "<p>Custom exception class raised when invalid codes are found that cannot be resolved by processing</p>\n", "bases": "builtins.Exception"}, "acmc.parse.InvalidCodesException.__init__": {"fullname": "acmc.parse.InvalidCodesException.__init__", "modulename": "acmc.parse", "qualname": "InvalidCodesException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">error</span></span>)</span>"}, "acmc.parse.InvalidCodesException.error": {"fullname": "acmc.parse.InvalidCodesException.error", "modulename": "acmc.parse", "qualname": "InvalidCodesException.error", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Proto": {"fullname": "acmc.parse.Proto", "modulename": "acmc.parse", "qualname": "Proto", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n"}, "acmc.parse.Proto.__init__": {"fullname": "acmc.parse.Proto.__init__", "modulename": "acmc.parse", "qualname": "Proto.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">name</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">trud_codes_path</span><span class=\"p\">:</span> <span class=\"n\">Optional</span><span class=\"p\">[</span><span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span><span class=\"p\">]</span> <span class=\"o\">=</span> <span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.Proto.checks": {"fullname": "acmc.parse.Proto.checks", "modulename": "acmc.parse", "qualname": "Proto.checks", "kind": "variable", "doc": "<p></p>\n", "annotation": ": list[tuple[str, typing.Callable[[pandas.core.frame.DataFrame], pandas.core.series.Series], typing.Callable[[pandas.core.frame.DataFrame, pathlib.Path], pandas.core.frame.DataFrame]]]"}, "acmc.parse.Proto.name": {"fullname": "acmc.parse.Proto.name", "modulename": "acmc.parse", "qualname": "Proto.name", "kind": "variable", "doc": "<p></p>\n", "annotation": ": str"}, "acmc.parse.Proto.raise_exception": {"fullname": "acmc.parse.Proto.raise_exception", "modulename": "acmc.parse", "qualname": "Proto.raise_exception", "kind": "function", "doc": "<p>Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">ex</span><span class=\"p\">:</span> <span class=\"ne\">Exception</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Proto.in_database": {"fullname": "acmc.parse.Proto.in_database", "modulename": "acmc.parse", "qualname": "Proto.in_database", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">db</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">col</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.process": {"fullname": "acmc.parse.Proto.process", "modulename": "acmc.parse", "qualname": "Proto.process", "kind": "function", "doc": "<p>identify issues that do not pass and fix them with define/d process</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.verify": {"fullname": "acmc.parse.Proto.verify", "modulename": "acmc.parse", "qualname": "Proto.verify", "kind": "function", "doc": "<p>verify codes in codes file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Read2": {"fullname": "acmc.parse.Read2", "modulename": "acmc.parse", "qualname": "Read2", "kind": "class", "doc": "<p>This Read2 class extends Proto, adding custom validation checks for a dataset of \"Read2\" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary.</p>\n", "bases": "Proto"}, "acmc.parse.Read2.checks": {"fullname": "acmc.parse.Read2.checks", "modulename": "acmc.parse", "qualname": "Read2.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Read3": {"fullname": "acmc.parse.Read3", "modulename": "acmc.parse", "qualname": "Read3", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Read3.checks": {"fullname": "acmc.parse.Read3.checks", "modulename": "acmc.parse", "qualname": "Read3.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Icd10": {"fullname": "acmc.parse.Icd10", "modulename": "acmc.parse", "qualname": "Icd10", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Icd10.checks": {"fullname": "acmc.parse.Icd10.checks", "modulename": "acmc.parse", "qualname": "Icd10.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Snomed": {"fullname": "acmc.parse.Snomed", "modulename": "acmc.parse", "qualname": "Snomed", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Snomed.checks": {"fullname": "acmc.parse.Snomed.checks", "modulename": "acmc.parse", "qualname": "Snomed.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Opcs4": {"fullname": "acmc.parse.Opcs4", "modulename": "acmc.parse", "qualname": "Opcs4", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Opcs4.checks": {"fullname": "acmc.parse.Opcs4.checks", "modulename": "acmc.parse", "qualname": "Opcs4.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Atc": {"fullname": "acmc.parse.Atc", "modulename": "acmc.parse", "qualname": "Atc", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Atc.checks": {"fullname": "acmc.parse.Atc.checks", "modulename": "acmc.parse", "qualname": "Atc.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Med": {"fullname": "acmc.parse.Med", "modulename": "acmc.parse", "qualname": "Med", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Med.checks": {"fullname": "acmc.parse.Med.checks", "modulename": "acmc.parse", "qualname": "Med.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Cprd": {"fullname": "acmc.parse.Cprd", "modulename": "acmc.parse", "qualname": "Cprd", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Cprd.checks": {"fullname": "acmc.parse.Cprd.checks", "modulename": "acmc.parse", "qualname": "Cprd.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.CodeTypeParser": {"fullname": "acmc.parse.CodeTypeParser", "modulename": "acmc.parse", "qualname": "CodeTypeParser", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodeTypeParser.__init__": {"fullname": "acmc.parse.CodeTypeParser.__init__", "modulename": "acmc.parse", "qualname": "CodeTypeParser.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">trud_processed_dir</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span> <span class=\"o\">=</span> <span class=\"n\">PosixPath</span><span class=\"p\">(</span><span class=\"s1\">&#39;vocab/trud/processed&#39;</span><span class=\"p\">)</span></span>)</span>"}, "acmc.parse.CodeTypeParser.code_types": {"fullname": "acmc.parse.CodeTypeParser.code_types", "modulename": "acmc.parse", "qualname": "CodeTypeParser.code_types", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen": {"fullname": "acmc.phen", "modulename": "acmc.phen", "kind": "module", "doc": "<h1 id=\"phenotype-module\">Phenotype Module</h1>\n\n<p>This module provides functionality for managing phenotypes.</p>\n"}, "acmc.phen.logger": {"fullname": "acmc.phen.logger", "modulename": "acmc.phen", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "&lt;Logger acmc_logger (INFO)&gt;"}, "acmc.phen.PHEN_DIR": {"fullname": "acmc.phen.PHEN_DIR", "modulename": "acmc.phen", "qualname": "PHEN_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;phen&#x27;"}, "acmc.phen.DEFAULT_PHEN_PATH": {"fullname": "acmc.phen.DEFAULT_PHEN_PATH", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;workspace/phen&#x27;)"}, "acmc.phen.CONCEPTS_DIR": {"fullname": "acmc.phen.CONCEPTS_DIR", "modulename": "acmc.phen", "qualname": "CONCEPTS_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;concepts&#x27;"}, "acmc.phen.MAP_DIR": {"fullname": "acmc.phen.MAP_DIR", "modulename": "acmc.phen", "qualname": "MAP_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;map&#x27;"}, "acmc.phen.CONCEPT_SET_DIR": {"fullname": "acmc.phen.CONCEPT_SET_DIR", "modulename": "acmc.phen", "qualname": "CONCEPT_SET_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;concept-sets&#x27;"}, "acmc.phen.CSV_PATH": {"fullname": "acmc.phen.CSV_PATH", "modulename": "acmc.phen", "qualname": "CSV_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;concept-sets/csv&#x27;)"}, "acmc.phen.OMOP_PATH": {"fullname": "acmc.phen.OMOP_PATH", "modulename": "acmc.phen", "qualname": "OMOP_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;concept-sets/omop&#x27;)"}, "acmc.phen.DEFAULT_PHEN_DIR_LIST": {"fullname": "acmc.phen.DEFAULT_PHEN_DIR_LIST", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_DIR_LIST", "kind": "variable", "doc": "<p></p>\n", "default_value": "[&#x27;concepts&#x27;, &#x27;map&#x27;, &#x27;concept-sets&#x27;]"}, "acmc.phen.CONFIG_FILE": {"fullname": "acmc.phen.CONFIG_FILE", "modulename": "acmc.phen", "qualname": "CONFIG_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;config.yaml&#x27;"}, "acmc.phen.VOCAB_VERSION_FILE": {"fullname": "acmc.phen.VOCAB_VERSION_FILE", "modulename": "acmc.phen", "qualname": "VOCAB_VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;vocab_version.yaml&#x27;"}, "acmc.phen.SEMANTIC_VERSION_TYPES": {"fullname": "acmc.phen.SEMANTIC_VERSION_TYPES", "modulename": "acmc.phen", "qualname": "SEMANTIC_VERSION_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "[&#x27;major&#x27;, &#x27;minor&#x27;, &#x27;patch&#x27;]"}, "acmc.phen.DEFAULT_VERSION_INC": {"fullname": "acmc.phen.DEFAULT_VERSION_INC", "modulename": "acmc.phen", "qualname": "DEFAULT_VERSION_INC", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;patch&#x27;"}, "acmc.phen.DEFAULT_GIT_BRANCH": {"fullname": "acmc.phen.DEFAULT_GIT_BRANCH", "modulename": "acmc.phen", "qualname": "DEFAULT_GIT_BRANCH", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;main&#x27;"}, "acmc.phen.SPLIT_COL_ACTION": {"fullname": "acmc.phen.SPLIT_COL_ACTION", "modulename": "acmc.phen", "qualname": "SPLIT_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;split_col&#x27;"}, "acmc.phen.CODES_COL_ACTION": {"fullname": "acmc.phen.CODES_COL_ACTION", "modulename": "acmc.phen", "qualname": "CODES_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;codes_col&#x27;"}, "acmc.phen.DIVIDE_COL_ACTION": {"fullname": "acmc.phen.DIVIDE_COL_ACTION", "modulename": "acmc.phen", "qualname": "DIVIDE_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;divide_col&#x27;"}, "acmc.phen.COL_ACTIONS": {"fullname": "acmc.phen.COL_ACTIONS", "modulename": "acmc.phen", "qualname": "COL_ACTIONS", "kind": "variable", "doc": "<p></p>\n", "default_value": "[&#x27;split_col&#x27;, &#x27;codes_col&#x27;, &#x27;divide_col&#x27;]"}, "acmc.phen.CODE_FILE_TYPES": {"fullname": "acmc.phen.CODE_FILE_TYPES", "modulename": "acmc.phen", "qualname": "CODE_FILE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "[&#x27;.xlsx&#x27;, &#x27;.xls&#x27;, &#x27;.csv&#x27;]"}, "acmc.phen.SOURCE_COL_SUFFIX": {"fullname": "acmc.phen.SOURCE_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "SOURCE_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;_acmc_source&#x27;"}, "acmc.phen.TARGET_COL_SUFFIX": {"fullname": "acmc.phen.TARGET_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "TARGET_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;_acmc_target&#x27;"}, "acmc.phen.CONFIG_SCHEMA": {"fullname": "acmc.phen.CONFIG_SCHEMA", "modulename": "acmc.phen", "qualname": "CONFIG_SCHEMA", "kind": "variable", "doc": "<p></p>\n", "default_value": "{&#x27;phenotype&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: True, &#x27;schema&#x27;: {&#x27;version&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True, &#x27;regex&#x27;: &#x27;^\\\\d+\\\\.\\\\d+\\\\.\\\\d+$&#x27;}, &#x27;omop&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: True, &#x27;schema&#x27;: {&#x27;vocabulary_id&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True}, &#x27;vocabulary_name&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True}, &#x27;vocabulary_reference&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True, &#x27;regex&#x27;: &#x27;^https?://.*&#x27;}}}, &#x27;map&#x27;: {&#x27;type&#x27;: &#x27;list&#x27;, &#x27;schema&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;allowed&#x27;: [&#x27;snomed&#x27;, &#x27;opcs4&#x27;, &#x27;read2&#x27;, &#x27;icd10&#x27;, &#x27;atc&#x27;, &#x27;read3&#x27;]}}, &#x27;concept_sets&#x27;: {&#x27;type&#x27;: &#x27;list&#x27;, &#x27;required&#x27;: True, &#x27;schema&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;schema&#x27;: {&#x27;name&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True}, &#x27;file&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: False, &#x27;schema&#x27;: {&#x27;path&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;, &#x27;required&#x27;: True}, &#x27;columns&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: True}, &#x27;category&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;}, &#x27;actions&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;schema&#x27;: {&#x27;divide_col&#x27;: {&#x27;type&#x27;: &#x27;string&#x27;}}}}}, &#x27;metadata&#x27;: {&#x27;type&#x27;: &#x27;dict&#x27;, &#x27;required&#x27;: True}}}}}}}"}, "acmc.phen.PhenValidationException": {"fullname": "acmc.phen.PhenValidationException", "modulename": "acmc.phen", "qualname": "PhenValidationException", "kind": "class", "doc": "<p>Custom exception class raised when validation errors in phenotype configuration file</p>\n", "bases": "builtins.Exception"}, "acmc.phen.PhenValidationException.__init__": {"fullname": "acmc.phen.PhenValidationException.__init__", "modulename": "acmc.phen", "qualname": "PhenValidationException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">validation_errors</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.phen.PhenValidationException.validation_errors": {"fullname": "acmc.phen.PhenValidationException.validation_errors", "modulename": "acmc.phen", "qualname": "PhenValidationException.validation_errors", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen.construct_git_url": {"fullname": "acmc.phen.construct_git_url", "modulename": "acmc.phen", "qualname": "construct_git_url", "kind": "function", "doc": "<p>Constructs a git url for github or gitlab including a PAT token environment variable</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.create_empty_git_dir": {"fullname": "acmc.phen.create_empty_git_dir", "modulename": "acmc.phen", "qualname": "create_empty_git_dir", "kind": "function", "doc": "<p>Creates a directory with a .gitkeep file so that it's tracked in git</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.check_delete_dir": {"fullname": "acmc.phen.check_delete_dir", "modulename": "acmc.phen", "qualname": "check_delete_dir", "kind": "function", "doc": "<p>Checks on the command line if a user wants to delete a directory</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>path (Path):</strong>  path of the directory to be deleted</li>\n<li><strong>msg (str):</strong>  message to be displayed to the user</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n  <p>Boolean: True if deleted</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.fork": {"fullname": "acmc.phen.fork", "modulename": "acmc.phen", "qualname": "fork", "kind": "function", "doc": "<p>Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin\"</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>phen_dir (str):</strong>  local directory path where the upstream repo is to be cloned</li>\n<li><strong>upstream_url (str):</strong>  url to the upstream repo</li>\n<li><strong>upstream_version (str):</strong>  version in the upstream repo to clone</li>\n<li><strong>new_origin_url (str, optional):</strong>  url of the remote repo to set as the new origin. Defaults to None.</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>ValueError:</strong>  if the specified version is not in the upstream repo</li>\n<li><strong>ValueError:</strong>  if the upstream repo is not a valid phenotype repo</li>\n<li><strong>ValueError:</strong>  if there's any other problems with Git</li>\n</ul>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">new_origin_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.init": {"fullname": "acmc.phen.init", "modulename": "acmc.phen", "qualname": "init", "kind": "function", "doc": "<p>Initial phenotype directory as git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.validate": {"fullname": "acmc.phen.validate", "modulename": "acmc.phen", "qualname": "validate", "kind": "function", "doc": "<p>Validates the phenotype directory is a git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.read_table_file": {"fullname": "acmc.phen.read_table_file", "modulename": "acmc.phen", "qualname": "read_table_file", "kind": "function", "doc": "<p>Load Code List File</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">excel_sheet</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">&#39;&#39;</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.process_actions": {"fullname": "acmc.phen.process_actions", "modulename": "acmc.phen", "qualname": "process_actions", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.preprocess_source_concepts": {"fullname": "acmc.phen.preprocess_source_concepts", "modulename": "acmc.phen", "qualname": "preprocess_source_concepts", "kind": "function", "doc": "<p>Parses each column individually - Order and length will not be preserved!</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">code_file_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.get_code_type_from_col_name": {"fullname": "acmc.phen.get_code_type_from_col_name", "modulename": "acmc.phen", "qualname": "get_code_type_from_col_name", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">col_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.translate_codes": {"fullname": "acmc.phen.translate_codes", "modulename": "acmc.phen", "qualname": "translate_codes", "kind": "function", "doc": "<p>Translates each source code type the source coding list into a target type and returns all conversions as a concept set</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">source_df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">concept_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.sql_row_exist": {"fullname": "acmc.phen.sql_row_exist", "modulename": "acmc.phen", "qualname": "sql_row_exist", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">conn</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Connection</span>, </span><span class=\"param\"><span class=\"n\">table</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">column</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">value</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.write_code_errors": {"fullname": "acmc.phen.write_code_errors", "modulename": "acmc.phen", "qualname": "write_code_errors", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">code_errors</span><span class=\"p\">:</span> <span class=\"nb\">list</span>, </span><span class=\"param\"><span class=\"n\">code_errors_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.write_vocab_version": {"fullname": "acmc.phen.write_vocab_version", "modulename": "acmc.phen", "qualname": "write_vocab_version", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map": {"fullname": "acmc.phen.map", "modulename": "acmc.phen", "qualname": "map", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map_target_code_type": {"fullname": "acmc.phen.map_target_code_type", "modulename": "acmc.phen", "qualname": "map_target_code_type", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">phenotype</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.generate_version_tag": {"fullname": "acmc.phen.generate_version_tag", "modulename": "acmc.phen", "qualname": "generate_version_tag", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">repo</span><span class=\"p\">:</span> <span class=\"n\">git</span><span class=\"o\">.</span><span class=\"n\">repo</span><span class=\"o\">.</span><span class=\"n\">base</span><span class=\"o\">.</span><span class=\"n\">Repo</span>,</span><span class=\"param\">\t<span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">&#39;patch&#39;</span>,</span><span class=\"param\">\t<span class=\"n\">use_v_prefix</span><span class=\"p\">:</span> <span class=\"nb\">bool</span> <span class=\"o\">=</span> <span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.publish": {"fullname": "acmc.phen.publish", "modulename": "acmc.phen", "qualname": "publish", "kind": "function", "doc": "<p>Publishes updates to the phenotype by commiting all changes to the repo directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">&#39;patch&#39;</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.export": {"fullname": "acmc.phen.export", "modulename": "acmc.phen", "qualname": "export", "kind": "function", "doc": "<p>Exports a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.copy": {"fullname": "acmc.phen.copy", "modulename": "acmc.phen", "qualname": "copy", "kind": "function", "doc": "<p>Copys a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.extract_concepts": {"fullname": "acmc.phen.extract_concepts", "modulename": "acmc.phen", "qualname": "extract_concepts", "kind": "function", "doc": "<p>Extracts concepts as {name: file_path} dictionary and a name set.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">config_data</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"nb\">dict</span><span class=\"p\">,</span> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"nb\">str</span><span class=\"p\">]]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.extract_clean_deepdiff_keys": {"fullname": "acmc.phen.extract_clean_deepdiff_keys", "modulename": "acmc.phen", "qualname": "extract_clean_deepdiff_keys", "kind": "function", "doc": "<p>Extracts clean keys from a DeepDiff dictionary.</p>\n\n<h6 id=\"parameters\">Parameters</h6>\n\n<ul>\n<li><strong>diff</strong>:  DeepDiff result dictionary</li>\n<li><strong>key_type</strong>:  The type of change to extract (e.g., \"dictionary_item_added\", \"dictionary_item_removed\")</li>\n</ul>\n\n<h6 id=\"returns\">Returns</h6>\n\n<blockquote>\n  <p>A set of clean key names</p>\n</blockquote>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">diff</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">key_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"n\">Any</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_config": {"fullname": "acmc.phen.diff_config", "modulename": "acmc.phen", "qualname": "diff_config", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">new_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_map_files": {"fullname": "acmc.phen.diff_map_files", "modulename": "acmc.phen", "qualname": "diff_map_files", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">new_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_phen": {"fullname": "acmc.phen.diff_phen", "modulename": "acmc.phen", "qualname": "diff_phen", "kind": "function", "doc": "<p>Compare the differences between two versions of a phenotype</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">new_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">new_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">old_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">report_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.diff": {"fullname": "acmc.phen.diff", "modulename": "acmc.phen", "qualname": "diff", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud": {"fullname": "acmc.trud", "modulename": "acmc.trud", "kind": "module", "doc": "<p></p>\n"}, "acmc.trud.logger": {"fullname": "acmc.trud.logger", "modulename": "acmc.trud", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "&lt;Logger acmc_logger (INFO)&gt;"}, "acmc.trud.FQDN": {"fullname": "acmc.trud.FQDN", "modulename": "acmc.trud", "qualname": "FQDN", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;isd.digital.nhs.uk&#x27;"}, "acmc.trud.VOCAB_PATH": {"fullname": "acmc.trud.VOCAB_PATH", "modulename": "acmc.trud", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/trud&#x27;)"}, "acmc.trud.VERSION_FILE": {"fullname": "acmc.trud.VERSION_FILE", "modulename": "acmc.trud", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "&#x27;trud_version.yaml&#x27;"}, "acmc.trud.VERSION_PATH": {"fullname": "acmc.trud.VERSION_PATH", "modulename": "acmc.trud", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/trud/trud_version.yaml&#x27;)"}, "acmc.trud.DOWNLOADS_PATH": {"fullname": "acmc.trud.DOWNLOADS_PATH", "modulename": "acmc.trud", "qualname": "DOWNLOADS_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/trud/downloads&#x27;)"}, "acmc.trud.PROCESSED_PATH": {"fullname": "acmc.trud.PROCESSED_PATH", "modulename": "acmc.trud", "qualname": "PROCESSED_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath(&#x27;vocab/trud/processed&#x27;)"}, "acmc.trud.get_releases": {"fullname": "acmc.trud.get_releases", "modulename": "acmc.trud", "qualname": "get_releases", "kind": "function", "doc": "<p>Retrieve release information for an item from the TRUD API.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">API_KEY</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">latest</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">list</span>:</span></span>", "funcdef": "def"}, "acmc.trud.download_release_file": {"fullname": "acmc.trud.download_release_file", "modulename": "acmc.trud", "qualname": "download_release_file", "kind": "function", "doc": "<p>Download specified file type for a given release of an item.</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release_ordinal</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">file_json_prefix</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.trud.validate_download_hash": {"fullname": "acmc.trud.validate_download_hash", "modulename": "acmc.trud", "qualname": "validate_download_hash", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">item_hash</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.unzip_download": {"fullname": "acmc.trud.unzip_download", "modulename": "acmc.trud", "qualname": "unzip_download", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_icd10": {"fullname": "acmc.trud.extract_icd10", "modulename": "acmc.trud", "qualname": "extract_icd10", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_opsc4": {"fullname": "acmc.trud.extract_opsc4", "modulename": "acmc.trud", "qualname": "extract_opsc4", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_data_migrations": {"fullname": "acmc.trud.extract_nhs_data_migrations", "modulename": "acmc.trud", "qualname": "extract_nhs_data_migrations", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_read_browser": {"fullname": "acmc.trud.extract_nhs_read_browser", "modulename": "acmc.trud", "qualname": "extract_nhs_read_browser", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.create_map_directories": {"fullname": "acmc.trud.create_map_directories", "modulename": "acmc.trud", "qualname": "create_map_directories", "kind": "function", "doc": "<p>Create map directories.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.install": {"fullname": "acmc.trud.install", "modulename": "acmc.trud", "qualname": "install", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.util": {"fullname": "acmc.util", "modulename": "acmc.util", "kind": "module", "doc": "<p></p>\n"}, "acmc.util.QuotedDumper": {"fullname": "acmc.util.QuotedDumper", "modulename": "acmc.util", "qualname": "QuotedDumper", "kind": "class", "doc": "<p></p>\n", "bases": "yaml.dumper.Dumper"}, "acmc.util.QuotedDumper.increase_indent": {"fullname": "acmc.util.QuotedDumper.increase_indent", "modulename": "acmc.util", "qualname": "QuotedDumper.increase_indent", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">flow</span><span class=\"o\">=</span><span class=\"kc\">False</span>, </span><span class=\"param\"><span class=\"n\">indentless</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}}, "docInfo": {"acmc": {"qualname": 0, "fullname": 1, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config": {"qualname": 0, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 39}, "acmc.logging_config.DEFAULT_LOG_FILE": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config.setup_logger": {"qualname": 2, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 24, "bases": 0, "doc": 16}, "acmc.logging_config.set_log_level": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 17, "bases": 0, "doc": 11}, "acmc.main": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.trud_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_clear": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_delete": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_init": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_fork": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_validate": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_map": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_export": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_publish": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_copy": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_diff": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.main": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 7, "bases": 0, "doc": 3}, "acmc.omop": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 15}, "acmc.omop.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VOCAB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_CDM_Version": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_DB_FILENAME": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.DB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, 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"h": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "e": {"docs": {"acmc.omop.export": {"tf": 1}, "acmc.phen.fork": {"tf": 1}}, "df": 2}}, "n": {"docs": {"acmc.parse.InvalidCodesException": {"tf": 1}, "acmc.parse.Read2": {"tf": 1}, "acmc.phen.PhenValidationException": {"tf": 1}}, "df": 3}}, "a": {"docs": {}, "df": 0, "t": {"docs": {"acmc.parse.Proto": {"tf": 1}, "acmc.parse.Read3": {"tf": 1}, "acmc.parse.Icd10": {"tf": 1}, "acmc.parse.Snomed": {"tf": 1}, "acmc.parse.Opcs4": {"tf": 1}, "acmc.parse.Atc": {"tf": 1}, "acmc.parse.Med": {"tf": 1}, "acmc.parse.Cprd": {"tf": 1}}, "df": 8}}}, "i": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "h": {"docs": {"acmc.parse.Proto.process": {"tf": 1}, "acmc.phen.create_empty_git_dir": {"tf": 1}, "acmc.phen.fork": {"tf": 1}, "acmc.phen.init": {"tf": 1}, "acmc.phen.validate": {"tf": 1}}, "df": 5}}, "l": {"docs": {}, "df": 0, "l": {"docs": {"acmc.phen.preprocess_source_concepts": {"tf": 1}}, "df": 1}}}, "a": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "t": {"docs": {}, "df": 0, "s": {"docs": {"acmc.phen.check_delete_dir": {"tf": 1}}, "df": 1}}}}}, "q": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "y": {"docs": {"acmc.omop.table_exists": {"tf": 1}, "acmc.omop.vocab_exists": {"tf": 1}, "acmc.omop.concept_set_exist": {"tf": 1}}, "df": 3}}}}}, "g": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1, "i": {"docs": {}, "df": 0, "t": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}, "acmc.phen.create_empty_git_dir": {"tf": 1}, "acmc.phen.fork": {"tf": 1}, "acmc.phen.init": {"tf": 1}, "acmc.phen.validate": {"tf": 1}}, "df": 5, "h": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "b": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}}, "df": 1}}}, "l": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "b": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}}, "df": 1}}}, "k": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "p": {"docs": {"acmc.phen.create_empty_git_dir": {"tf": 1}}, "df": 1}}}}}, "v": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {"acmc.trud.download_release_file": {"tf": 1}}, "df": 1}}}}}, "k": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "y": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1.4142135623730951}}, "df": 1, "s": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1}}}}}}}, "pipeline": ["trimmer"], "_isPrebuiltIndex": true};
 
     // mirrored in build-search-index.js (part 1)
     // Also split on html tags. this is a cheap heuristic, but good enough.
diff --git a/pyproject.toml b/pyproject.toml
index e535e66b3153c8c7149674f2b33b34c082195cb1..70612d2bbc389cd043bc31ba956dbd09ac78b3a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -83,7 +83,7 @@ dependencies = [
 [tool.hatch.envs.dev.scripts]
 format = "black ."
 type = "mypy ."
-docs = "pdoc -o docs/api -d markdown --docformat markdown --include-undocumented acmc"
+docs = "pdoc -o docs/api -d google --docformat google --include-undocumented acmc"
 precommit = "hatch run format && hatch run type && hatch run docs"
 
 [tool.hatch.build]