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<h2>API Documentation</h2>
<ul class="memberlist">
<li>
<a class="variable" href="#logger">logger</a>
</li>
<li>
<a class="variable" href="#SUPPORTED_CODE_TYPES">SUPPORTED_CODE_TYPES</a>
</li>
<li>
<a class="class" href="#CodesError">CodesError</a>
<ul class="memberlist">
<li>
<a class="function" href="#CodesError.__init__">CodesError</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#InvalidCodesException">InvalidCodesException</a>
<ul class="memberlist">
<li>
<a class="function" href="#InvalidCodesException.__init__">InvalidCodesException</a>
</li>
<li>
<a class="variable" href="#InvalidCodesException.error">error</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#Proto">Proto</a>
<ul class="memberlist">
<li>
<a class="function" href="#Proto.__init__">Proto</a>
</li>
<li>
<a class="variable" href="#Proto.checks">checks</a>
</li>
<li>
<a class="variable" href="#Proto.name">name</a> </li>
<li>
<a class="function" href="#Proto.raise_exception">raise_exception</a>
</li>
<li>
<a class="function" href="#Proto.in_database">in_database</a>
</li>
<li>
<a class="function" href="#Proto.process">process</a>
</li>
<li>
<a class="function" href="#Proto.verify">verify</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#Read2">Read2</a>
<ul class="memberlist">
<li>
<a class="variable" href="#Read2.checks">checks</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#Read3">Read3</a>
<ul class="memberlist">
<li>
<a class="variable" href="#Read3.checks">checks</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#Icd10">Icd10</a>
<ul class="memberlist">
<li>
<a class="variable" href="#Icd10.checks">checks</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#Snomed">Snomed</a>
<ul class="memberlist">
<li>
<a class="variable" href="#Snomed.checks">checks</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#Opcs4">Opcs4</a>
<ul class="memberlist">
<li>
<a class="variable" href="#Opcs4.checks">checks</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#Atc">Atc</a>
<ul class="memberlist">
<li>
<a class="variable" href="#Atc.checks">checks</a>
</li>
</ul>
</li> <li>
<a class="class" href="#Med">Med</a>
<ul class="memberlist">
<li>
<a class="variable" href="#Med.checks">checks</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#Cprd">Cprd</a>
<ul class="memberlist">
<li>
<a class="variable" href="#Cprd.checks">checks</a>
</li>
</ul>
</li>
<li>
<a class="class" href="#CodeTypeParser">CodeTypeParser</a>
<ul class="memberlist">
<li>
<a class="function" href="#CodeTypeParser.__init__">CodeTypeParser</a>
</li>
<li>
<a class="variable" href="#CodeTypeParser.code_types">code_types</a>
</li>
</ul>
</li>
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<h1 class="modulename">
<a href="./../acmc.html">acmc</a><wbr>.parse </h1>
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<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">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Callable</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Tuple</span>
</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
</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="kn">from</span><span class="w"> </span><span class="nn">acmc</span><span class="w"> </span><span class="kn">import</span> <span class="n">trud</span><span class="p">,</span> <span class="n">logging_config</span> <span class="k">as</span> <span class="n">lc</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="c1"># setup logging</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">lc</span><span class="o">.</span><span class="n">setup_logger</span><span class="p">()</span>
</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a>
</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="c1"># Define allowed values</span>
</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="n">SUPPORTED_CODE_TYPES</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"icd10"</span><span class="p">,</span> <span class="s2">"snomed"</span><span class="p">,</span> <span class="s2">"opcs4"</span><span class="p">,</span> <span class="s2">"atc"</span><span class="p">}</span>
</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a>
</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">class</span><span class="w"> </span><span class="nc">CodesError</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">"""A class used in InvalidCodesException to report an error if a code parser check fails"""</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="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="n">codes</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">codes_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">code_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span></span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a> <span class="c1"># initialise class variables with provided parameters</span>
</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a> <span class="k">if</span> <span class="n">key</span> <span class="o">!=</span> <span class="s2">"self"</span><span class="p">:</span>
</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a> <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a>
</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a>
</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="k">class</span><span class="w"> </span><span class="nc">InvalidCodesException</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a><span class="w"> </span><span class="sd">"""Custom exception class raised when invalid codes are found that cannot be resolved by processing"""</span>
</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a>
</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">error</span><span class="p">):</span>
</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">error</span><span class="o">.</span><span class="n">message</span><span class="p">)</span>
</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="n">error</span>
</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a>
</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a>
</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Proto</span><span class="p">:</span>
</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a><span class="w"> </span><span class="sd">"""</span>
</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a><span class="sd"> Define checks as list of 3 tuple: (Message, Condition, Process)</span>
</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a><span class="sd"> - Message = The name of the condition (what is printed and logged)</span>
</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="sd"> - Condition = True if Passed, and False if Failed</span>
</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a><span class="sd"> - Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</span>
</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="sd"> """</span>
</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a>
</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a> <span class="n">checks</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span>
</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a> <span class="nb">tuple</span><span class="p">[</span>
</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a> <span class="nb">str</span><span class="p">,</span> <span class="c1"># The description, e.g., "Not Empty"</span>
</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a> <span class="n">Callable</span><span class="p">[</span>
</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a> <span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">],</span>
</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">,</span>
</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a> <span class="p">],</span> <span class="c1"># The first lambda function: takes a list and returns a pd.Series of booleans</span>
</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a> <span class="n">Callable</span><span class="p">[</span>
</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a> <span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">Path</span><span class="p">],</span>
</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span>
</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a> <span class="p">],</span> <span class="c1"># The second lambda function: takes a list and a string, and returns nothing</span>
</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a> <span class="p">]</span>
</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="p">]</span>
</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a>
</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud_codes_path</span>
</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">)</span>
</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a> <span class="sa">f</span><span class="s2">"Error: Read2 code file '</span><span class="si">{</span><span class="n">trud_codes_path</span><span class="si">}</span><span class="s2">' does not exist. Please ensure you have installed TRUD correctly"</span>
</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a> <span class="p">)</span>
</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a>
</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">name</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="k">def</span><span class="w"> </span><span class="nf">raise_exception</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ex</span><span class="p">:</span> <span class="ne">Exception</span><span class="p">):</span>
</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a><span class="w"> </span><span class="sd">"""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"""</span>
</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a> <span class="k">raise</span> <span class="n">ex</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="k">def</span><span class="w"> </span><span class="nf">in_database</span><span class="p">(</span>
</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">col</span><span class="p">:</span> <span class="nb">str</span>
</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="p">)</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-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="k">return</span> <span class="n">codes</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">db</span><span class="p">[</span><span class="n">col</span><span class="p">])</span>
</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a>
</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">process</span><span class="p">(</span>
</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span>
</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</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 id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a><span class="w"> </span><span class="sd">"""identify issues that do not pass and fix them with define/d process"""</span>
</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="n">errors</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="c1"># Iter through each item in check.</span>
</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">fix</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="c1"># Check if any codes fail the check to False</span>
</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span><span class="o">.</span><span class="n">all</span><span class="p">():</span>
</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="c1"># Log the number of codes that failed</span>
</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="sa">f</span><span class="s2">"Check: </span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="p">(</span><span class="o">~</span><span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">))</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span><span class="si">}</span><span class="s2"> failed, trying to fix"</span>
</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a> <span class="p">)</span></span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a> <span class="c1"># try fix errors by running lamba "process" function</span>
</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a> <span class="k">try</span><span class="p">:</span>
</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">fix</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">)</span>
</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</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">"Check: Fixed"</span><span class="p">)</span>
</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="k">except</span> <span class="n">InvalidCodesException</span> <span class="k">as</span> <span class="n">ex</span><span class="p">:</span>
</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="n">errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ex</span><span class="o">.</span><span class="n">error</span><span class="p">)</span>
</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</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">"Check: passed"</span><span class="p">)</span>
</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a>
</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a> <span class="k">return</span> <span class="n">codes</span><span class="p">,</span> <span class="n">errors</span>
</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a>
</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">verify</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a><span class="w"> </span><span class="sd">"""verify codes in codes file"""</span>
</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([])</span>
</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a>
</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a> <span class="c1"># Iter through each item in check.</span>
</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">process</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a> <span class="c1"># run conditional check</span>
</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span>
</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">conds</span><span class="p">,</span> <span class="n">out</span><span class="o">.</span><span class="n">all</span><span class="p">())</span>
</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a>
</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a> <span class="k">return</span> <span class="n">conds</span>
</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a>
</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a>
</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Read2</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a><span class="w"> </span><span class="sd">"""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."""</span>
</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a>
</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"read2"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2.parquet"</span><span class="p">)</span>
</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a>
</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="c1"># validate checks</span>
</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="p">(</span>
</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="c1"># check codes are not empty, if empty throw an exception</span>
</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="p">)</span>
</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> <span class="p">)</span>
</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a> <span class="p">),</span>
</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> <span class="p">),</span>
</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a> <span class="p">(</span>
</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a> <span class="c1"># check codes <5 characters, if too short pads it with . (dots) to reach 5 characters</span>
</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">5</span><span class="p">),</span>
</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">pad</span><span class="p">(</span>
</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a> <span class="n">width</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">side</span><span class="o">=</span><span class="s2">"right"</span><span class="p">,</span> <span class="n">fillchar</span><span class="o">=</span><span class="s2">"."</span>
</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a> <span class="p">),</span>
</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="p">),</span>
</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a> <span class="p">(</span>
</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> <span class="c1"># check codes > 5 characters, If too long, truncates them to 5 characters</span>
</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">5</span><span class="p">),</span>
</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">5</span><span class="p">],</span>
</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a> <span class="p">),</span>
</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> <span class="p">(</span>
</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> <span class="c1"># checks codes contain numbers, or dots (.), if not logs invalid code error</span>
</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a> <span class="s2">"Alphanumeric Dot"</span><span class="p">,</span>
</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a> <span class="sa">f</span><span class="s2">"Illegal code format, not alphanumeric dot"</span><span class="p">,</span></span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a> <span class="p">)</span>
</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a> <span class="p">)</span>
</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a> <span class="p">),</span>
</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a> <span class="p">),</span>
</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a> <span class="p">(</span>
</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a> <span class="c1"># checks code exists in self.db (the Read2 dataset). If missing log invalid codes.</span>
</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="sa">f</span><span class="s2">"Codes do not exist in database"</span><span class="p">,</span>
</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="p">)</span>
</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a> <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-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="p">),</span>
</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="p">]</span>
</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a>
</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">class</span><span class="w"> </span><span class="nc">Read3</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"Read3"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3.parquet"</span><span class="p">)</span>
</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a>
</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a> <span class="p">(</span>
</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="p">)</span>
</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a> <span class="p">)</span>
</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="p">),</span>
</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a> <span class="p">),</span>
</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a> <span class="p">(</span>
</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">5</span><span class="p">),</span>
</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">pad</span><span class="p">(</span>
</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a> <span class="n">width</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">side</span><span class="o">=</span><span class="s2">"right"</span><span class="p">,</span> <span class="n">fillchar</span><span class="o">=</span><span class="s2">"."</span>
</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a> <span class="p">),</span>
</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a> <span class="p">),</span>
</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a> <span class="p">(</span>
</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">5</span><span class="p">),</span>
</span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">5</span><span class="p">],</span>
</span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a> <span class="p">),</span>
</span><span id="L-219"><a href="#L-219"><span class="linenos">219</span></a> <span class="p">(</span>
</span><span id="L-220"><a href="#L-220"><span class="linenos">220</span></a> <span class="s2">"Alphanumeric Dot"</span><span class="p">,</span>
</span><span id="L-221"><a href="#L-221"><span class="linenos">221</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
</span><span id="L-222"><a href="#L-222"><span class="linenos">222</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-223"><a href="#L-223"><span class="linenos">223</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-224"><a href="#L-224"><span class="linenos">224</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-225"><a href="#L-225"><span class="linenos">225</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Dot"</span><span class="p">,</span>
</span><span id="L-226"><a href="#L-226"><span class="linenos">226</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-227"><a href="#L-227"><span class="linenos">227</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-228"><a href="#L-228"><span class="linenos">228</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
</span><span id="L-229"><a href="#L-229"><span class="linenos">229</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span></span><span id="L-230"><a href="#L-230"><span class="linenos">230</span></a> <span class="p">)</span>
</span><span id="L-231"><a href="#L-231"><span class="linenos">231</span></a> <span class="p">)</span>
</span><span id="L-232"><a href="#L-232"><span class="linenos">232</span></a> <span class="p">),</span>
</span><span id="L-233"><a href="#L-233"><span class="linenos">233</span></a> <span class="p">),</span>
</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a> <span class="p">(</span>
</span><span id="L-235"><a href="#L-235"><span class="linenos">235</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="L-236"><a href="#L-236"><span class="linenos">236</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="L-237"><a href="#L-237"><span class="linenos">237</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-238"><a href="#L-238"><span class="linenos">238</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-239"><a href="#L-239"><span class="linenos">239</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-240"><a href="#L-240"><span class="linenos">240</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
</span><span id="L-241"><a href="#L-241"><span class="linenos">241</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-242"><a href="#L-242"><span class="linenos">242</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-243"><a href="#L-243"><span class="linenos">243</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="L-244"><a href="#L-244"><span class="linenos">244</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</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><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 class="p">),</span>
</span><span id="L-248"><a href="#L-248"><span class="linenos">248</span></a> <span class="p">),</span>
</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a> <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><span id="L-252"><a href="#L-252"><span class="linenos">252</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Icd10</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="L-253"><a href="#L-253"><span class="linenos">253</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="L-254"><a href="#L-254"><span class="linenos">254</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"icd10"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"icd10.parquet"</span><span class="p">)</span>
</span><span id="L-255"><a href="#L-255"><span class="linenos">255</span></a>
</span><span id="L-256"><a href="#L-256"><span class="linenos">256</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="L-257"><a href="#L-257"><span class="linenos">257</span></a> <span class="p">(</span>
</span><span id="L-258"><a href="#L-258"><span class="linenos">258</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="L-259"><a href="#L-259"><span class="linenos">259</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="L-260"><a href="#L-260"><span class="linenos">260</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-261"><a href="#L-261"><span class="linenos">261</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-262"><a href="#L-262"><span class="linenos">262</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-263"><a href="#L-263"><span class="linenos">263</span></a> <span class="sa">f</span><span class="s2">"Code list is empty </span><span class="si">{</span><span class="n">codes_file</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
</span><span id="L-264"><a href="#L-264"><span class="linenos">264</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-265"><a href="#L-265"><span class="linenos">265</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-266"><a href="#L-266"><span class="linenos">266</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="L-267"><a href="#L-267"><span class="linenos">267</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-268"><a href="#L-268"><span class="linenos">268</span></a> <span class="p">)</span>
</span><span id="L-269"><a href="#L-269"><span class="linenos">269</span></a> <span class="p">)</span>
</span><span id="L-270"><a href="#L-270"><span class="linenos">270</span></a> <span class="p">),</span>
</span><span id="L-271"><a href="#L-271"><span class="linenos">271</span></a> <span class="p">),</span>
</span><span id="L-272"><a href="#L-272"><span class="linenos">272</span></a> <span class="p">(</span>
</span><span id="L-273"><a href="#L-273"><span class="linenos">273</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
</span><span id="L-274"><a href="#L-274"><span class="linenos">274</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">3</span><span class="p">),</span>
</span><span id="L-275"><a href="#L-275"><span class="linenos">275</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-276"><a href="#L-276"><span class="linenos">276</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-277"><a href="#L-277"><span class="linenos">277</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-278"><a href="#L-278"><span class="linenos">278</span></a> <span class="sa">f</span><span class="s2">"QA Too Short"</span><span class="p">,</span>
</span><span id="L-279"><a href="#L-279"><span class="linenos">279</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-280"><a href="#L-280"><span class="linenos">280</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-281"><a href="#L-281"><span class="linenos">281</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">3</span><span class="p">),</span>
</span><span id="L-282"><a href="#L-282"><span class="linenos">282</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-283"><a href="#L-283"><span class="linenos">283</span></a> <span class="p">)</span>
</span><span id="L-284"><a href="#L-284"><span class="linenos">284</span></a> <span class="p">)</span>
</span><span id="L-285"><a href="#L-285"><span class="linenos">285</span></a> <span class="p">),</span>
</span><span id="L-286"><a href="#L-286"><span class="linenos">286</span></a> <span class="p">),</span>
</span><span id="L-287"><a href="#L-287"><span class="linenos">287</span></a> <span class="p">(</span>
</span><span id="L-288"><a href="#L-288"><span class="linenos">288</span></a> <span class="s2">"Has Dot"</span><span class="p">,</span>
</span><span id="L-289"><a href="#L-289"><span class="linenos">289</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">".*\..*"</span><span class="p">)),</span> <span class="c1"># check if contains dot</span>
</span><span id="L-290"><a href="#L-290"><span class="linenos">290</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
</span><span id="L-291"><a href="#L-291"><span class="linenos">291</span></a> <span class="s2">"."</span><span class="p">,</span> <span class="s2">""</span>
</span><span id="L-292"><a href="#L-292"><span class="linenos">292</span></a> <span class="p">),</span> <span class="c1"># delete any dots in string</span>
</span><span id="L-293"><a href="#L-293"><span class="linenos">293</span></a> <span class="c1"># lambda codes : codes.str.split('\.').apply(lambda ls: ls[0]) #only get part before dot</span>
</span><span id="L-294"><a href="#L-294"><span class="linenos">294</span></a> <span class="p">),</span>
</span><span id="L-295"><a href="#L-295"><span class="linenos">295</span></a> <span class="p">(</span>
</span><span id="L-296"><a href="#L-296"><span class="linenos">296</span></a> <span class="s2">"Alphanumeric Capital"</span><span class="p">,</span>
</span><span id="L-297"><a href="#L-297"><span class="linenos">297</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
</span><span id="L-298"><a href="#L-298"><span class="linenos">298</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-299"><a href="#L-299"><span class="linenos">299</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span></span><span id="L-300"><a href="#L-300"><span class="linenos">300</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-301"><a href="#L-301"><span class="linenos">301</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Capital"</span><span class="p">,</span>
</span><span id="L-302"><a href="#L-302"><span class="linenos">302</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-303"><a href="#L-303"><span class="linenos">303</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-304"><a href="#L-304"><span class="linenos">304</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
</span><span id="L-305"><a href="#L-305"><span class="linenos">305</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><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="p">),</span>
</span><span id="L-309"><a href="#L-309"><span class="linenos">309</span></a> <span class="p">),</span>
</span><span id="L-310"><a href="#L-310"><span class="linenos">310</span></a> <span class="p">(</span>
</span><span id="L-311"><a href="#L-311"><span class="linenos">311</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="L-312"><a href="#L-312"><span class="linenos">312</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span>
</span><span id="L-313"><a href="#L-313"><span class="linenos">313</span></a> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
</span><span id="L-314"><a href="#L-314"><span class="linenos">314</span></a> <span class="o">&</span> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s2">"_alt"</span><span class="p">)</span>
</span><span id="L-315"><a href="#L-315"><span class="linenos">315</span></a> <span class="p">),</span>
</span><span id="L-316"><a href="#L-316"><span class="linenos">316</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-317"><a href="#L-317"><span class="linenos">317</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-318"><a href="#L-318"><span class="linenos">318</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-319"><a href="#L-319"><span class="linenos">319</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
</span><span id="L-320"><a href="#L-320"><span class="linenos">320</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-321"><a href="#L-321"><span class="linenos">321</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-322"><a href="#L-322"><span class="linenos">322</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span>
</span><span id="L-323"><a href="#L-323"><span class="linenos">323</span></a> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
</span><span id="L-324"><a href="#L-324"><span class="linenos">324</span></a> <span class="o">&</span> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s2">"_alt"</span><span class="p">)</span>
</span><span id="L-325"><a href="#L-325"><span class="linenos">325</span></a> <span class="p">),</span>
</span><span id="L-326"><a href="#L-326"><span class="linenos">326</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-327"><a href="#L-327"><span class="linenos">327</span></a> <span class="p">)</span>
</span><span id="L-328"><a href="#L-328"><span class="linenos">328</span></a> <span class="p">)</span>
</span><span id="L-329"><a href="#L-329"><span class="linenos">329</span></a> <span class="p">),</span>
</span><span id="L-330"><a href="#L-330"><span class="linenos">330</span></a> <span class="p">),</span>
</span><span id="L-331"><a href="#L-331"><span class="linenos">331</span></a> <span class="c1"># (</span>
</span><span id="L-332"><a href="#L-332"><span class="linenos">332</span></a> <span class="c1"># "ICD10 Regex",</span>
</span><span id="L-333"><a href="#L-333"><span class="linenos">333</span></a> <span class="c1"># lambda codes : codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Alpha, Num, Num , Dot?, 4xAlphNum*</span>
</span><span id="L-334"><a href="#L-334"><span class="linenos">334</span></a> <span class="c1"># lambda codes : lc.log_invalid_code(codes,</span>
</span><span id="L-335"><a href="#L-335"><span class="linenos">335</span></a> <span class="c1"># codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Log non-matching rows</span>
</span><span id="L-336"><a href="#L-336"><span class="linenos">336</span></a> <span class="c1"># code_type="icd10",</span>
</span><span id="L-337"><a href="#L-337"><span class="linenos">337</span></a> <span class="c1">#</span>
</span><span id="L-338"><a href="#L-338"><span class="linenos">338</span></a> <span class="c1"># )</span>
</span><span id="L-339"><a href="#L-339"><span class="linenos">339</span></a> <span class="p">]</span>
</span><span id="L-340"><a href="#L-340"><span class="linenos">340</span></a>
</span><span id="L-341"><a href="#L-341"><span class="linenos">341</span></a>
</span><span id="L-342"><a href="#L-342"><span class="linenos">342</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Snomed</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="L-343"><a href="#L-343"><span class="linenos">343</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="L-344"><a href="#L-344"><span class="linenos">344</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"snomed"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"snomed.parquet"</span><span class="p">)</span>
</span><span id="L-345"><a href="#L-345"><span class="linenos">345</span></a>
</span><span id="L-346"><a href="#L-346"><span class="linenos">346</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="L-347"><a href="#L-347"><span class="linenos">347</span></a> <span class="c1"># (</span>
</span><span id="L-348"><a href="#L-348"><span class="linenos">348</span></a> <span class="c1"># "Not Empty",</span>
</span><span id="L-349"><a href="#L-349"><span class="linenos">349</span></a> <span class="c1"># lambda codes : pd.Series([len(codes) > 0]),</span>
</span><span id="L-350"><a href="#L-350"><span class="linenos">350</span></a> <span class="c1"># lambda codes : raise_exception(Exception("Code List is Empty"))</span>
</span><span id="L-351"><a href="#L-351"><span class="linenos">351</span></a> <span class="c1"># ),</span>
</span><span id="L-352"><a href="#L-352"><span class="linenos">352</span></a> <span class="p">(</span>
</span><span id="L-353"><a href="#L-353"><span class="linenos">353</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
</span><span id="L-354"><a href="#L-354"><span class="linenos">354</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">6</span><span class="p">),</span>
</span><span id="L-355"><a href="#L-355"><span class="linenos">355</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-356"><a href="#L-356"><span class="linenos">356</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-357"><a href="#L-357"><span class="linenos">357</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-358"><a href="#L-358"><span class="linenos">358</span></a> <span class="sa">f</span><span class="s2">"QA Too Short"</span><span class="p">,</span>
</span><span id="L-359"><a href="#L-359"><span class="linenos">359</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-360"><a href="#L-360"><span class="linenos">360</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-361"><a href="#L-361"><span class="linenos">361</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">6</span><span class="p">),</span>
</span><span id="L-362"><a href="#L-362"><span class="linenos">362</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-363"><a href="#L-363"><span class="linenos">363</span></a> <span class="p">)</span>
</span><span id="L-364"><a href="#L-364"><span class="linenos">364</span></a> <span class="p">)</span>
</span><span id="L-365"><a href="#L-365"><span class="linenos">365</span></a> <span class="p">),</span>
</span><span id="L-366"><a href="#L-366"><span class="linenos">366</span></a> <span class="p">),</span>
</span><span id="L-367"><a href="#L-367"><span class="linenos">367</span></a> <span class="p">(</span>
</span><span id="L-368"><a href="#L-368"><span class="linenos">368</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
</span><span id="L-369"><a href="#L-369"><span class="linenos">369</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">18</span><span class="p">),</span></span><span id="L-370"><a href="#L-370"><span class="linenos">370</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-371"><a href="#L-371"><span class="linenos">371</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-372"><a href="#L-372"><span class="linenos">372</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-373"><a href="#L-373"><span class="linenos">373</span></a> <span class="sa">f</span><span class="s2">"QA Too Long"</span><span class="p">,</span>
</span><span id="L-374"><a href="#L-374"><span class="linenos">374</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-375"><a href="#L-375"><span class="linenos">375</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-376"><a href="#L-376"><span class="linenos">376</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">18</span><span class="p">),</span>
</span><span id="L-377"><a href="#L-377"><span class="linenos">377</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</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 class="p">)</span>
</span><span id="L-380"><a href="#L-380"><span class="linenos">380</span></a> <span class="p">),</span>
</span><span id="L-381"><a href="#L-381"><span class="linenos">381</span></a> <span class="p">),</span>
</span><span id="L-382"><a href="#L-382"><span class="linenos">382</span></a> <span class="p">(</span>
</span><span id="L-383"><a href="#L-383"><span class="linenos">383</span></a> <span class="s2">"Numeric"</span><span class="p">,</span>
</span><span id="L-384"><a href="#L-384"><span class="linenos">384</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[0-9]+$"</span><span class="p">),</span>
</span><span id="L-385"><a href="#L-385"><span class="linenos">385</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-386"><a href="#L-386"><span class="linenos">386</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-387"><a href="#L-387"><span class="linenos">387</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-388"><a href="#L-388"><span class="linenos">388</span></a> <span class="sa">f</span><span class="s2">"QA Numeric"</span><span class="p">,</span>
</span><span id="L-389"><a href="#L-389"><span class="linenos">389</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-390"><a href="#L-390"><span class="linenos">390</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-391"><a href="#L-391"><span class="linenos">391</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[0-9]+$"</span><span class="p">),</span>
</span><span id="L-392"><a href="#L-392"><span class="linenos">392</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-393"><a href="#L-393"><span class="linenos">393</span></a> <span class="p">)</span>
</span><span id="L-394"><a href="#L-394"><span class="linenos">394</span></a> <span class="p">)</span>
</span><span id="L-395"><a href="#L-395"><span class="linenos">395</span></a> <span class="p">),</span>
</span><span id="L-396"><a href="#L-396"><span class="linenos">396</span></a> <span class="p">),</span>
</span><span id="L-397"><a href="#L-397"><span class="linenos">397</span></a> <span class="c1"># (</span>
</span><span id="L-398"><a href="#L-398"><span class="linenos">398</span></a> <span class="c1"># "Is Integer",</span>
</span><span id="L-399"><a href="#L-399"><span class="linenos">399</span></a> <span class="c1"># lambda codes : codes.dtype == int,</span>
</span><span id="L-400"><a href="#L-400"><span class="linenos">400</span></a> <span class="c1"># lambda codes : codes.astype(int) #Convert to integer</span>
</span><span id="L-401"><a href="#L-401"><span class="linenos">401</span></a> <span class="c1"># ),</span>
</span><span id="L-402"><a href="#L-402"><span class="linenos">402</span></a> <span class="p">(</span>
</span><span id="L-403"><a href="#L-403"><span class="linenos">403</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="L-404"><a href="#L-404"><span class="linenos">404</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="L-405"><a href="#L-405"><span class="linenos">405</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-406"><a href="#L-406"><span class="linenos">406</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-407"><a href="#L-407"><span class="linenos">407</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-408"><a href="#L-408"><span class="linenos">408</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
</span><span id="L-409"><a href="#L-409"><span class="linenos">409</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-410"><a href="#L-410"><span class="linenos">410</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-411"><a href="#L-411"><span class="linenos">411</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="L-412"><a href="#L-412"><span class="linenos">412</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-413"><a href="#L-413"><span class="linenos">413</span></a> <span class="p">)</span>
</span><span id="L-414"><a href="#L-414"><span class="linenos">414</span></a> <span class="p">)</span>
</span><span id="L-415"><a href="#L-415"><span class="linenos">415</span></a> <span class="p">),</span>
</span><span id="L-416"><a href="#L-416"><span class="linenos">416</span></a> <span class="p">),</span>
</span><span id="L-417"><a href="#L-417"><span class="linenos">417</span></a> <span class="p">]</span>
</span><span id="L-418"><a href="#L-418"><span class="linenos">418</span></a>
</span><span id="L-419"><a href="#L-419"><span class="linenos">419</span></a>
</span><span id="L-420"><a href="#L-420"><span class="linenos">420</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Opcs4</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="L-421"><a href="#L-421"><span class="linenos">421</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="L-422"><a href="#L-422"><span class="linenos">422</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"opcs4"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"opcs4.parquet"</span><span class="p">)</span>
</span><span id="L-423"><a href="#L-423"><span class="linenos">423</span></a>
</span><span id="L-424"><a href="#L-424"><span class="linenos">424</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="L-425"><a href="#L-425"><span class="linenos">425</span></a> <span class="p">(</span>
</span><span id="L-426"><a href="#L-426"><span class="linenos">426</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="L-427"><a href="#L-427"><span class="linenos">427</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="L-428"><a href="#L-428"><span class="linenos">428</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-429"><a href="#L-429"><span class="linenos">429</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-430"><a href="#L-430"><span class="linenos">430</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-431"><a href="#L-431"><span class="linenos">431</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="L-432"><a href="#L-432"><span class="linenos">432</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-433"><a href="#L-433"><span class="linenos">433</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-434"><a href="#L-434"><span class="linenos">434</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="L-435"><a href="#L-435"><span class="linenos">435</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-436"><a href="#L-436"><span class="linenos">436</span></a> <span class="p">)</span>
</span><span id="L-437"><a href="#L-437"><span class="linenos">437</span></a> <span class="p">)</span>
</span><span id="L-438"><a href="#L-438"><span class="linenos">438</span></a> <span class="p">),</span>
</span><span id="L-439"><a href="#L-439"><span class="linenos">439</span></a> <span class="p">),</span></span><span id="L-440"><a href="#L-440"><span class="linenos">440</span></a> <span class="p">(</span>
</span><span id="L-441"><a href="#L-441"><span class="linenos">441</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="L-442"><a href="#L-442"><span class="linenos">442</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="L-443"><a href="#L-443"><span class="linenos">443</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-444"><a href="#L-444"><span class="linenos">444</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-445"><a href="#L-445"><span class="linenos">445</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-446"><a href="#L-446"><span class="linenos">446</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
</span><span id="L-447"><a href="#L-447"><span class="linenos">447</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-448"><a href="#L-448"><span class="linenos">448</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-449"><a href="#L-449"><span class="linenos">449</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="L-450"><a href="#L-450"><span class="linenos">450</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-451"><a href="#L-451"><span class="linenos">451</span></a> <span class="p">)</span>
</span><span id="L-452"><a href="#L-452"><span class="linenos">452</span></a> <span class="p">)</span>
</span><span id="L-453"><a href="#L-453"><span class="linenos">453</span></a> <span class="p">),</span>
</span><span id="L-454"><a href="#L-454"><span class="linenos">454</span></a> <span class="p">),</span>
</span><span id="L-455"><a href="#L-455"><span class="linenos">455</span></a> <span class="p">]</span>
</span><span id="L-456"><a href="#L-456"><span class="linenos">456</span></a>
</span><span id="L-457"><a href="#L-457"><span class="linenos">457</span></a>
</span><span id="L-458"><a href="#L-458"><span class="linenos">458</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Atc</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="L-459"><a href="#L-459"><span class="linenos">459</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="L-460"><a href="#L-460"><span class="linenos">460</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"atc"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
</span><span id="L-461"><a href="#L-461"><span class="linenos">461</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="L-462"><a href="#L-462"><span class="linenos">462</span></a> <span class="p">(</span>
</span><span id="L-463"><a href="#L-463"><span class="linenos">463</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="L-464"><a href="#L-464"><span class="linenos">464</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="L-465"><a href="#L-465"><span class="linenos">465</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-466"><a href="#L-466"><span class="linenos">466</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-467"><a href="#L-467"><span class="linenos">467</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-468"><a href="#L-468"><span class="linenos">468</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="L-469"><a href="#L-469"><span class="linenos">469</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-470"><a href="#L-470"><span class="linenos">470</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-471"><a href="#L-471"><span class="linenos">471</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="L-472"><a href="#L-472"><span class="linenos">472</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-473"><a href="#L-473"><span class="linenos">473</span></a> <span class="p">)</span>
</span><span id="L-474"><a href="#L-474"><span class="linenos">474</span></a> <span class="p">)</span>
</span><span id="L-475"><a href="#L-475"><span class="linenos">475</span></a> <span class="p">),</span>
</span><span id="L-476"><a href="#L-476"><span class="linenos">476</span></a> <span class="p">),</span>
</span><span id="L-477"><a href="#L-477"><span class="linenos">477</span></a> <span class="p">(</span>
</span><span id="L-478"><a href="#L-478"><span class="linenos">478</span></a> <span class="s2">"Alphanumeric Capital"</span><span class="p">,</span>
</span><span id="L-479"><a href="#L-479"><span class="linenos">479</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
</span><span id="L-480"><a href="#L-480"><span class="linenos">480</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-481"><a href="#L-481"><span class="linenos">481</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-482"><a href="#L-482"><span class="linenos">482</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-483"><a href="#L-483"><span class="linenos">483</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Capital"</span><span class="p">,</span>
</span><span id="L-484"><a href="#L-484"><span class="linenos">484</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-485"><a href="#L-485"><span class="linenos">485</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-486"><a href="#L-486"><span class="linenos">486</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
</span><span id="L-487"><a href="#L-487"><span class="linenos">487</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-488"><a href="#L-488"><span class="linenos">488</span></a> <span class="p">)</span>
</span><span id="L-489"><a href="#L-489"><span class="linenos">489</span></a> <span class="p">)</span>
</span><span id="L-490"><a href="#L-490"><span class="linenos">490</span></a> <span class="p">),</span>
</span><span id="L-491"><a href="#L-491"><span class="linenos">491</span></a> <span class="p">),</span>
</span><span id="L-492"><a href="#L-492"><span class="linenos">492</span></a> <span class="p">]</span>
</span><span id="L-493"><a href="#L-493"><span class="linenos">493</span></a>
</span><span id="L-494"><a href="#L-494"><span class="linenos">494</span></a>
</span><span id="L-495"><a href="#L-495"><span class="linenos">495</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Med</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="L-496"><a href="#L-496"><span class="linenos">496</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="L-497"><a href="#L-497"><span class="linenos">497</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"med"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
</span><span id="L-498"><a href="#L-498"><span class="linenos">498</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="L-499"><a href="#L-499"><span class="linenos">499</span></a> <span class="p">(</span>
</span><span id="L-500"><a href="#L-500"><span class="linenos">500</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="L-501"><a href="#L-501"><span class="linenos">501</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="L-502"><a href="#L-502"><span class="linenos">502</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-503"><a href="#L-503"><span class="linenos">503</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-504"><a href="#L-504"><span class="linenos">504</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-505"><a href="#L-505"><span class="linenos">505</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="L-506"><a href="#L-506"><span class="linenos">506</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-507"><a href="#L-507"><span class="linenos">507</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-508"><a href="#L-508"><span class="linenos">508</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="L-509"><a href="#L-509"><span class="linenos">509</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span></span><span id="L-510"><a href="#L-510"><span class="linenos">510</span></a> <span class="p">)</span>
</span><span id="L-511"><a href="#L-511"><span class="linenos">511</span></a> <span class="p">)</span>
</span><span id="L-512"><a href="#L-512"><span class="linenos">512</span></a> <span class="p">),</span>
</span><span id="L-513"><a href="#L-513"><span class="linenos">513</span></a> <span class="p">)</span>
</span><span id="L-514"><a href="#L-514"><span class="linenos">514</span></a> <span class="p">]</span>
</span><span id="L-515"><a href="#L-515"><span class="linenos">515</span></a>
</span><span id="L-516"><a href="#L-516"><span class="linenos">516</span></a>
</span><span id="L-517"><a href="#L-517"><span class="linenos">517</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Cprd</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="L-518"><a href="#L-518"><span class="linenos">518</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="L-519"><a href="#L-519"><span class="linenos">519</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"cprd"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
</span><span id="L-520"><a href="#L-520"><span class="linenos">520</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="L-521"><a href="#L-521"><span class="linenos">521</span></a> <span class="p">(</span>
</span><span id="L-522"><a href="#L-522"><span class="linenos">522</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="L-523"><a href="#L-523"><span class="linenos">523</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="L-524"><a href="#L-524"><span class="linenos">524</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="L-525"><a href="#L-525"><span class="linenos">525</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="L-526"><a href="#L-526"><span class="linenos">526</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="L-527"><a href="#L-527"><span class="linenos">527</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="L-528"><a href="#L-528"><span class="linenos">528</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="L-529"><a href="#L-529"><span class="linenos">529</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="L-530"><a href="#L-530"><span class="linenos">530</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="L-531"><a href="#L-531"><span class="linenos">531</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="L-532"><a href="#L-532"><span class="linenos">532</span></a> <span class="p">)</span>
</span><span id="L-533"><a href="#L-533"><span class="linenos">533</span></a> <span class="p">)</span>
</span><span id="L-534"><a href="#L-534"><span class="linenos">534</span></a> <span class="p">),</span>
</span><span id="L-535"><a href="#L-535"><span class="linenos">535</span></a> <span class="p">)</span>
</span><span id="L-536"><a href="#L-536"><span class="linenos">536</span></a> <span class="p">]</span>
</span><span id="L-537"><a href="#L-537"><span class="linenos">537</span></a>
</span><span id="L-538"><a href="#L-538"><span class="linenos">538</span></a>
</span><span id="L-539"><a href="#L-539"><span class="linenos">539</span></a><span class="k">class</span><span class="w"> </span><span class="nc">CodeTypeParser</span><span class="p">:</span>
</span><span id="L-540"><a href="#L-540"><span class="linenos">540</span></a><span class="w"> </span><span class="sd">"""A class used in InvalidCodesException to report an error if a code parser check fails"""</span>
</span><span id="L-541"><a href="#L-541"><span class="linenos">541</span></a>
</span><span id="L-542"><a href="#L-542"><span class="linenos">542</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trud_processed_dir</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span><span class="p">):</span>
</span><span id="L-543"><a href="#L-543"><span class="linenos">543</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
</span><span id="L-544"><a href="#L-544"><span class="linenos">544</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
</span><span id="L-545"><a href="#L-545"><span class="linenos">545</span></a> <span class="sa">f</span><span class="s2">"Cannot initialise parsers as the TRUD processed directory </span><span class="si">{</span><span class="n">trud_processed_dir</span><span class="si">}</span><span class="s2"> does not exist, please check that TRUD has been installed: acmc trud install"</span>
</span><span id="L-546"><a href="#L-546"><span class="linenos">546</span></a> <span class="p">)</span>
</span><span id="L-547"><a href="#L-547"><span class="linenos">547</span></a>
</span><span id="L-548"><a href="#L-548"><span class="linenos">548</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">code_types</span> <span class="o">=</span> <span class="p">{</span>
</span><span id="L-549"><a href="#L-549"><span class="linenos">549</span></a> <span class="s2">"read2"</span><span class="p">:</span> <span class="n">Read2</span><span class="p">(),</span>
</span><span id="L-550"><a href="#L-550"><span class="linenos">550</span></a> <span class="s2">"read3"</span><span class="p">:</span> <span class="n">Read3</span><span class="p">(),</span>
</span><span id="L-551"><a href="#L-551"><span class="linenos">551</span></a> <span class="s2">"icd10"</span><span class="p">:</span> <span class="n">Icd10</span><span class="p">(),</span>
</span><span id="L-552"><a href="#L-552"><span class="linenos">552</span></a> <span class="s2">"snomed"</span><span class="p">:</span> <span class="n">Snomed</span><span class="p">(),</span>
</span><span id="L-553"><a href="#L-553"><span class="linenos">553</span></a> <span class="s2">"opcs4"</span><span class="p">:</span> <span class="n">Opcs4</span><span class="p">(),</span>
</span><span id="L-554"><a href="#L-554"><span class="linenos">554</span></a> <span class="s2">"atc"</span><span class="p">:</span> <span class="n">Atc</span><span class="p">(),</span>
</span><span id="L-555"><a href="#L-555"><span class="linenos">555</span></a> <span class="s2">"med"</span><span class="p">:</span> <span class="n">Med</span><span class="p">(),</span>
</span><span id="L-556"><a href="#L-556"><span class="linenos">556</span></a> <span class="s2">"cprd"</span><span class="p">:</span> <span class="n">Cprd</span><span class="p">(),</span>
</span><span id="L-557"><a href="#L-557"><span class="linenos">557</span></a> <span class="p">}</span>
</span></pre></div>
</section>
<section id="logger">
<div class="attr variable">
<span class="name">logger</span> =
<span class="default_value"><Logger acmc_logger (INFO)></span>
</div>
<a class="headerlink" href="#logger"></a>
</section>
<section id="SUPPORTED_CODE_TYPES">
<div class="attr variable">
<span class="name">SUPPORTED_CODE_TYPES</span> =
<span class="default_value">{'read2', 'read3', 'snomed', 'icd10', 'opcs4', 'atc'}</span>
</div>
<a class="headerlink" href="#SUPPORTED_CODE_TYPES"></a>
</section>
<section id="CodesError">
<input id="CodesError-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">CodesError</span>:
<label class="view-source-button" for="CodesError-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#CodesError"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="CodesError-17"><a href="#CodesError-17"><span class="linenos">17</span></a><span class="k">class</span><span class="w"> </span><span class="nc">CodesError</span><span class="p">:</span>
</span><span id="CodesError-18"><a href="#CodesError-18"><span class="linenos">18</span></a><span class="w"> </span><span class="sd">"""A class used in InvalidCodesException to report an error if a code parser check fails"""</span>
</span><span id="CodesError-19"><a href="#CodesError-19"><span class="linenos">19</span></a>
</span><span id="CodesError-20"><a href="#CodesError-20"><span class="linenos">20</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="n">codes</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">codes_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">code_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
</span><span id="CodesError-21"><a href="#CodesError-21"><span class="linenos">21</span></a> <span class="c1"># initialise class variables with provided parameters</span>
</span><span id="CodesError-22"><a href="#CodesError-22"><span class="linenos">22</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
</span><span id="CodesError-23"><a href="#CodesError-23"><span class="linenos">23</span></a> <span class="k">if</span> <span class="n">key</span> <span class="o">!=</span> <span class="s2">"self"</span><span class="p">:</span>
</span><span id="CodesError-24"><a href="#CodesError-24"><span class="linenos">24</span></a> <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
</span></pre></div>
<div class="docstring"><p>A class used in InvalidCodesException to report an error if a code parser check fails</p>
</div>
<div id="CodesError.__init__" class="classattr">
<input id="CodesError.__init__-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr function">
<span class="name">CodesError</span><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>
<label class="view-source-button" for="CodesError.__init__-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#CodesError.__init__"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="CodesError.__init__-20"><a href="#CodesError.__init__-20"><span class="linenos">20</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="n">codes</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">codes_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">code_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
</span><span id="CodesError.__init__-21"><a href="#CodesError.__init__-21"><span class="linenos">21</span></a> <span class="c1"># initialise class variables with provided parameters</span>
</span><span id="CodesError.__init__-22"><a href="#CodesError.__init__-22"><span class="linenos">22</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
</span><span id="CodesError.__init__-23"><a href="#CodesError.__init__-23"><span class="linenos">23</span></a> <span class="k">if</span> <span class="n">key</span> <span class="o">!=</span> <span class="s2">"self"</span><span class="p">:</span>
</span><span id="CodesError.__init__-24"><a href="#CodesError.__init__-24"><span class="linenos">24</span></a> <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
</span></pre></div>
</div>
</section>
<section id="InvalidCodesException">
<input id="InvalidCodesException-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">InvalidCodesException</span><wbr>(<span class="base">builtins.Exception</span>):
<label class="view-source-button" for="InvalidCodesException-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#InvalidCodesException"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="InvalidCodesException-27"><a href="#InvalidCodesException-27"><span class="linenos">27</span></a><span class="k">class</span><span class="w"> </span><span class="nc">InvalidCodesException</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
</span><span id="InvalidCodesException-28"><a href="#InvalidCodesException-28"><span class="linenos">28</span></a><span class="w"> </span><span class="sd">"""Custom exception class raised when invalid codes are found that cannot be resolved by processing"""</span>
</span><span id="InvalidCodesException-29"><a href="#InvalidCodesException-29"><span class="linenos">29</span></a>
</span><span id="InvalidCodesException-30"><a href="#InvalidCodesException-30"><span class="linenos">30</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">error</span><span class="p">):</span>
</span><span id="InvalidCodesException-31"><a href="#InvalidCodesException-31"><span class="linenos">31</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">error</span><span class="o">.</span><span class="n">message</span><span class="p">)</span></span><span id="InvalidCodesException-32"><a href="#InvalidCodesException-32"><span class="linenos">32</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="n">error</span>
</span></pre></div>
<div class="docstring"><p>Custom exception class raised when invalid codes are found that cannot be resolved by processing</p>
</div>
<div id="InvalidCodesException.__init__" class="classattr">
<input id="InvalidCodesException.__init__-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr function">
<span class="name">InvalidCodesException</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">error</span></span>)</span>
<label class="view-source-button" for="InvalidCodesException.__init__-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#InvalidCodesException.__init__"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="InvalidCodesException.__init__-30"><a href="#InvalidCodesException.__init__-30"><span class="linenos">30</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">error</span><span class="p">):</span>
</span><span id="InvalidCodesException.__init__-31"><a href="#InvalidCodesException.__init__-31"><span class="linenos">31</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">error</span><span class="o">.</span><span class="n">message</span><span class="p">)</span>
</span><span id="InvalidCodesException.__init__-32"><a href="#InvalidCodesException.__init__-32"><span class="linenos">32</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="n">error</span>
</span></pre></div>
</div>
<div id="InvalidCodesException.error" class="classattr">
<div class="attr variable">
<span class="name">error</span>
</div>
<a class="headerlink" href="#InvalidCodesException.error"></a>
</div>
</section>
<section id="Proto">
<input id="Proto-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">Proto</span>:
<label class="view-source-button" for="Proto-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Proto"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Proto-35"><a href="#Proto-35"><span class="linenos"> 35</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Proto</span><span class="p">:</span>
</span><span id="Proto-36"><a href="#Proto-36"><span class="linenos"> 36</span></a><span class="w"> </span><span class="sd">"""</span>
</span><span id="Proto-37"><a href="#Proto-37"><span class="linenos"> 37</span></a><span class="sd"> Define checks as list of 3 tuple: (Message, Condition, Process)</span>
</span><span id="Proto-38"><a href="#Proto-38"><span class="linenos"> 38</span></a><span class="sd"> - Message = The name of the condition (what is printed and logged)</span>
</span><span id="Proto-39"><a href="#Proto-39"><span class="linenos"> 39</span></a><span class="sd"> - Condition = True if Passed, and False if Failed</span>
</span><span id="Proto-40"><a href="#Proto-40"><span class="linenos"> 40</span></a><span class="sd"> - Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</span>
</span><span id="Proto-41"><a href="#Proto-41"><span class="linenos"> 41</span></a><span class="sd"> """</span>
</span><span id="Proto-42"><a href="#Proto-42"><span class="linenos"> 42</span></a>
</span><span id="Proto-43"><a href="#Proto-43"><span class="linenos"> 43</span></a> <span class="n">checks</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span>
</span><span id="Proto-44"><a href="#Proto-44"><span class="linenos"> 44</span></a> <span class="nb">tuple</span><span class="p">[</span>
</span><span id="Proto-45"><a href="#Proto-45"><span class="linenos"> 45</span></a> <span class="nb">str</span><span class="p">,</span> <span class="c1"># The description, e.g., "Not Empty"</span>
</span><span id="Proto-46"><a href="#Proto-46"><span class="linenos"> 46</span></a> <span class="n">Callable</span><span class="p">[</span>
</span><span id="Proto-47"><a href="#Proto-47"><span class="linenos"> 47</span></a> <span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">],</span>
</span><span id="Proto-48"><a href="#Proto-48"><span class="linenos"> 48</span></a> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">,</span>
</span><span id="Proto-49"><a href="#Proto-49"><span class="linenos"> 49</span></a> <span class="p">],</span> <span class="c1"># The first lambda function: takes a list and returns a pd.Series of booleans</span>
</span><span id="Proto-50"><a href="#Proto-50"><span class="linenos"> 50</span></a> <span class="n">Callable</span><span class="p">[</span>
</span><span id="Proto-51"><a href="#Proto-51"><span class="linenos"> 51</span></a> <span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">Path</span><span class="p">],</span>
</span><span id="Proto-52"><a href="#Proto-52"><span class="linenos"> 52</span></a> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span>
</span><span id="Proto-53"><a href="#Proto-53"><span class="linenos"> 53</span></a> <span class="p">],</span> <span class="c1"># The second lambda function: takes a list and a string, and returns nothing</span>
</span><span id="Proto-54"><a href="#Proto-54"><span class="linenos"> 54</span></a> <span class="p">]</span></span><span id="Proto-55"><a href="#Proto-55"><span class="linenos"> 55</span></a> <span class="p">]</span>
</span><span id="Proto-56"><a href="#Proto-56"><span class="linenos"> 56</span></a>
</span><span id="Proto-57"><a href="#Proto-57"><span class="linenos"> 57</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
</span><span id="Proto-58"><a href="#Proto-58"><span class="linenos"> 58</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
</span><span id="Proto-59"><a href="#Proto-59"><span class="linenos"> 59</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
</span><span id="Proto-60"><a href="#Proto-60"><span class="linenos"> 60</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud_codes_path</span>
</span><span id="Proto-61"><a href="#Proto-61"><span class="linenos"> 61</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">)</span>
</span><span id="Proto-62"><a href="#Proto-62"><span class="linenos"> 62</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="Proto-63"><a href="#Proto-63"><span class="linenos"> 63</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
</span><span id="Proto-64"><a href="#Proto-64"><span class="linenos"> 64</span></a> <span class="sa">f</span><span class="s2">"Error: Read2 code file '</span><span class="si">{</span><span class="n">trud_codes_path</span><span class="si">}</span><span class="s2">' does not exist. Please ensure you have installed TRUD correctly"</span>
</span><span id="Proto-65"><a href="#Proto-65"><span class="linenos"> 65</span></a> <span class="p">)</span>
</span><span id="Proto-66"><a href="#Proto-66"><span class="linenos"> 66</span></a>
</span><span id="Proto-67"><a href="#Proto-67"><span class="linenos"> 67</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">name</span>
</span><span id="Proto-68"><a href="#Proto-68"><span class="linenos"> 68</span></a>
</span><span id="Proto-69"><a href="#Proto-69"><span class="linenos"> 69</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">raise_exception</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ex</span><span class="p">:</span> <span class="ne">Exception</span><span class="p">):</span>
</span><span id="Proto-70"><a href="#Proto-70"><span class="linenos"> 70</span></a><span class="w"> </span><span class="sd">"""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"""</span>
</span><span id="Proto-71"><a href="#Proto-71"><span class="linenos"> 71</span></a> <span class="k">raise</span> <span class="n">ex</span>
</span><span id="Proto-72"><a href="#Proto-72"><span class="linenos"> 72</span></a>
</span><span id="Proto-73"><a href="#Proto-73"><span class="linenos"> 73</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">in_database</span><span class="p">(</span>
</span><span id="Proto-74"><a href="#Proto-74"><span class="linenos"> 74</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">col</span><span class="p">:</span> <span class="nb">str</span>
</span><span id="Proto-75"><a href="#Proto-75"><span class="linenos"> 75</span></a> <span class="p">)</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="Proto-76"><a href="#Proto-76"><span class="linenos"> 76</span></a> <span class="k">return</span> <span class="n">codes</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">db</span><span class="p">[</span><span class="n">col</span><span class="p">])</span>
</span><span id="Proto-77"><a href="#Proto-77"><span class="linenos"> 77</span></a>
</span><span id="Proto-78"><a href="#Proto-78"><span class="linenos"> 78</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">process</span><span class="p">(</span>
</span><span id="Proto-79"><a href="#Proto-79"><span class="linenos"> 79</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span>
</span><span id="Proto-80"><a href="#Proto-80"><span class="linenos"> 80</span></a> <span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</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 id="Proto-81"><a href="#Proto-81"><span class="linenos"> 81</span></a><span class="w"> </span><span class="sd">"""identify issues that do not pass and fix them with define/d process"""</span>
</span><span id="Proto-82"><a href="#Proto-82"><span class="linenos"> 82</span></a> <span class="n">errors</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="Proto-83"><a href="#Proto-83"><span class="linenos"> 83</span></a> <span class="c1"># Iter through each item in check.</span>
</span><span id="Proto-84"><a href="#Proto-84"><span class="linenos"> 84</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">fix</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
</span><span id="Proto-85"><a href="#Proto-85"><span class="linenos"> 85</span></a> <span class="c1"># Check if any codes fail the check to False</span>
</span><span id="Proto-86"><a href="#Proto-86"><span class="linenos"> 86</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span><span class="o">.</span><span class="n">all</span><span class="p">():</span>
</span><span id="Proto-87"><a href="#Proto-87"><span class="linenos"> 87</span></a> <span class="c1"># Log the number of codes that failed</span>
</span><span id="Proto-88"><a href="#Proto-88"><span class="linenos"> 88</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
</span><span id="Proto-89"><a href="#Proto-89"><span class="linenos"> 89</span></a> <span class="sa">f</span><span class="s2">"Check: </span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="p">(</span><span class="o">~</span><span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">))</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span><span class="si">}</span><span class="s2"> failed, trying to fix"</span>
</span><span id="Proto-90"><a href="#Proto-90"><span class="linenos"> 90</span></a> <span class="p">)</span>
</span><span id="Proto-91"><a href="#Proto-91"><span class="linenos"> 91</span></a> <span class="c1"># try fix errors by running lamba "process" function</span>
</span><span id="Proto-92"><a href="#Proto-92"><span class="linenos"> 92</span></a> <span class="k">try</span><span class="p">:</span>
</span><span id="Proto-93"><a href="#Proto-93"><span class="linenos"> 93</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">fix</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">)</span>
</span><span id="Proto-94"><a href="#Proto-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">"Check: Fixed"</span><span class="p">)</span>
</span><span id="Proto-95"><a href="#Proto-95"><span class="linenos"> 95</span></a> <span class="k">except</span> <span class="n">InvalidCodesException</span> <span class="k">as</span> <span class="n">ex</span><span class="p">:</span>
</span><span id="Proto-96"><a href="#Proto-96"><span class="linenos"> 96</span></a> <span class="n">errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ex</span><span class="o">.</span><span class="n">error</span><span class="p">)</span>
</span><span id="Proto-97"><a href="#Proto-97"><span class="linenos"> 97</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="Proto-98"><a href="#Proto-98"><span class="linenos"> 98</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">"Check: passed"</span><span class="p">)</span>
</span><span id="Proto-99"><a href="#Proto-99"><span class="linenos"> 99</span></a>
</span><span id="Proto-100"><a href="#Proto-100"><span class="linenos">100</span></a> <span class="k">return</span> <span class="n">codes</span><span class="p">,</span> <span class="n">errors</span>
</span><span id="Proto-101"><a href="#Proto-101"><span class="linenos">101</span></a>
</span><span id="Proto-102"><a href="#Proto-102"><span class="linenos">102</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">verify</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
</span><span id="Proto-103"><a href="#Proto-103"><span class="linenos">103</span></a><span class="w"> </span><span class="sd">"""verify codes in codes file"""</span>
</span><span id="Proto-104"><a href="#Proto-104"><span class="linenos">104</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([])</span>
</span><span id="Proto-105"><a href="#Proto-105"><span class="linenos">105</span></a>
</span><span id="Proto-106"><a href="#Proto-106"><span class="linenos">106</span></a> <span class="c1"># Iter through each item in check.</span>
</span><span id="Proto-107"><a href="#Proto-107"><span class="linenos">107</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">process</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
</span><span id="Proto-108"><a href="#Proto-108"><span class="linenos">108</span></a> <span class="c1"># run conditional check</span>
</span><span id="Proto-109"><a href="#Proto-109"><span class="linenos">109</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span>
</span><span id="Proto-110"><a href="#Proto-110"><span class="linenos">110</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">conds</span><span class="p">,</span> <span class="n">out</span><span class="o">.</span><span class="n">all</span><span class="p">())</span>
</span><span id="Proto-111"><a href="#Proto-111"><span class="linenos">111</span></a>
</span><span id="Proto-112"><a href="#Proto-112"><span class="linenos">112</span></a> <span class="k">return</span> <span class="n">conds</span>
</span></pre></div>
<div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
<ul>
<li>Message = The name of the condition (what is printed and logged)</li>
<li>Condition = True if Passed, and False if Failed</li>
<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
</ul>
</div>
<div id="Proto.__init__" class="classattr">
<input id="Proto.__init__-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr function">
<span class="name">Proto</span><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>
<label class="view-source-button" for="Proto.__init__-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Proto.__init__"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Proto.__init__-57"><a href="#Proto.__init__-57"><span class="linenos">57</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
</span><span id="Proto.__init__-58"><a href="#Proto.__init__-58"><span class="linenos">58</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
</span><span id="Proto.__init__-59"><a href="#Proto.__init__-59"><span class="linenos">59</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
</span><span id="Proto.__init__-60"><a href="#Proto.__init__-60"><span class="linenos">60</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud_codes_path</span>
</span><span id="Proto.__init__-61"><a href="#Proto.__init__-61"><span class="linenos">61</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">)</span>
</span><span id="Proto.__init__-62"><a href="#Proto.__init__-62"><span class="linenos">62</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="Proto.__init__-63"><a href="#Proto.__init__-63"><span class="linenos">63</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
</span><span id="Proto.__init__-64"><a href="#Proto.__init__-64"><span class="linenos">64</span></a> <span class="sa">f</span><span class="s2">"Error: Read2 code file '</span><span class="si">{</span><span class="n">trud_codes_path</span><span class="si">}</span><span class="s2">' does not exist. Please ensure you have installed TRUD correctly"</span>
</span><span id="Proto.__init__-65"><a href="#Proto.__init__-65"><span class="linenos">65</span></a> <span class="p">)</span>
</span><span id="Proto.__init__-66"><a href="#Proto.__init__-66"><span class="linenos">66</span></a>
</span><span id="Proto.__init__-67"><a href="#Proto.__init__-67"><span class="linenos">67</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">name</span>
</span></pre></div>
</div>
<div id="Proto.checks" class="classattr">
<div class="attr variable">
<span class="name">checks</span><span class="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]]]</span>
</div>
<a class="headerlink" href="#Proto.checks"></a>
</div>
<div id="Proto.name" class="classattr">
<div class="attr variable">
<span class="name">name</span><span class="annotation">: str</span>
</div>
<a class="headerlink" href="#Proto.name"></a>
</div>
<div id="Proto.raise_exception" class="classattr">
<input id="Proto.raise_exception-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr function">
<span class="def">def</span>
<span class="name">raise_exception</span><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>
<label class="view-source-button" for="Proto.raise_exception-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Proto.raise_exception"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Proto.raise_exception-69"><a href="#Proto.raise_exception-69"><span class="linenos">69</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">raise_exception</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ex</span><span class="p">:</span> <span class="ne">Exception</span><span class="p">):</span>
</span><span id="Proto.raise_exception-70"><a href="#Proto.raise_exception-70"><span class="linenos">70</span></a><span class="w"> </span><span class="sd">"""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"""</span>
</span><span id="Proto.raise_exception-71"><a href="#Proto.raise_exception-71"><span class="linenos">71</span></a> <span class="k">raise</span> <span class="n">ex</span>
</span></pre></div>
<div class="docstring"><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>
</div>
</div>
<div id="Proto.in_database" class="classattr">
<input id="Proto.in_database-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr function">
<span class="def">def</span>
<span class="name">in_database</span><span class="signature pdoc-code multiline">(<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">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"> <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>
<label class="view-source-button" for="Proto.in_database-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Proto.in_database"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Proto.in_database-73"><a href="#Proto.in_database-73"><span class="linenos">73</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">in_database</span><span class="p">(</span>
</span><span id="Proto.in_database-74"><a href="#Proto.in_database-74"><span class="linenos">74</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">col</span><span class="p">:</span> <span class="nb">str</span>
</span><span id="Proto.in_database-75"><a href="#Proto.in_database-75"><span class="linenos">75</span></a> <span class="p">)</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="Proto.in_database-76"><a href="#Proto.in_database-76"><span class="linenos">76</span></a> <span class="k">return</span> <span class="n">codes</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">db</span><span class="p">[</span><span class="n">col</span><span class="p">])</span>
</span></pre></div>
</div>
<div id="Proto.process" class="classattr">
<input id="Proto.process-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr function">
<span class="def">def</span>
<span class="name">process</span><span class="signature pdoc-code multiline">(<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 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>
<label class="view-source-button" for="Proto.process-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Proto.process"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Proto.process-78"><a href="#Proto.process-78"><span class="linenos"> 78</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">process</span><span class="p">(</span>
</span><span id="Proto.process-79"><a href="#Proto.process-79"><span class="linenos"> 79</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span>
</span><span id="Proto.process-80"><a href="#Proto.process-80"><span class="linenos"> 80</span></a> <span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</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 id="Proto.process-81"><a href="#Proto.process-81"><span class="linenos"> 81</span></a><span class="w"> </span><span class="sd">"""identify issues that do not pass and fix them with define/d process"""</span>
</span><span id="Proto.process-82"><a href="#Proto.process-82"><span class="linenos"> 82</span></a> <span class="n">errors</span> <span class="o">=</span> <span class="p">[]</span>
</span><span id="Proto.process-83"><a href="#Proto.process-83"><span class="linenos"> 83</span></a> <span class="c1"># Iter through each item in check.</span>
</span><span id="Proto.process-84"><a href="#Proto.process-84"><span class="linenos"> 84</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">fix</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
</span><span id="Proto.process-85"><a href="#Proto.process-85"><span class="linenos"> 85</span></a> <span class="c1"># Check if any codes fail the check to False</span>
</span><span id="Proto.process-86"><a href="#Proto.process-86"><span class="linenos"> 86</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span><span class="o">.</span><span class="n">all</span><span class="p">():</span>
</span><span id="Proto.process-87"><a href="#Proto.process-87"><span class="linenos"> 87</span></a> <span class="c1"># Log the number of codes that failed</span>
</span><span id="Proto.process-88"><a href="#Proto.process-88"><span class="linenos"> 88</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
</span><span id="Proto.process-89"><a href="#Proto.process-89"><span class="linenos"> 89</span></a> <span class="sa">f</span><span class="s2">"Check: </span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="p">(</span><span class="o">~</span><span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">))</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span><span class="si">}</span><span class="s2"> failed, trying to fix"</span>
</span><span id="Proto.process-90"><a href="#Proto.process-90"><span class="linenos"> 90</span></a> <span class="p">)</span>
</span><span id="Proto.process-91"><a href="#Proto.process-91"><span class="linenos"> 91</span></a> <span class="c1"># try fix errors by running lamba "process" function</span>
</span><span id="Proto.process-92"><a href="#Proto.process-92"><span class="linenos"> 92</span></a> <span class="k">try</span><span class="p">:</span>
</span><span id="Proto.process-93"><a href="#Proto.process-93"><span class="linenos"> 93</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">fix</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">)</span>
</span><span id="Proto.process-94"><a href="#Proto.process-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">"Check: Fixed"</span><span class="p">)</span>
</span><span id="Proto.process-95"><a href="#Proto.process-95"><span class="linenos"> 95</span></a> <span class="k">except</span> <span class="n">InvalidCodesException</span> <span class="k">as</span> <span class="n">ex</span><span class="p">:</span>
</span><span id="Proto.process-96"><a href="#Proto.process-96"><span class="linenos"> 96</span></a> <span class="n">errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ex</span><span class="o">.</span><span class="n">error</span><span class="p">)</span>
</span><span id="Proto.process-97"><a href="#Proto.process-97"><span class="linenos"> 97</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="Proto.process-98"><a href="#Proto.process-98"><span class="linenos"> 98</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">"Check: passed"</span><span class="p">)</span>
</span><span id="Proto.process-99"><a href="#Proto.process-99"><span class="linenos"> 99</span></a>
</span><span id="Proto.process-100"><a href="#Proto.process-100"><span class="linenos">100</span></a> <span class="k">return</span> <span class="n">codes</span><span class="p">,</span> <span class="n">errors</span>
</span></pre></div>
<div class="docstring"><p>identify issues that do not pass and fix them with define/d process</p>
</div>
</div>
<div id="Proto.verify" class="classattr">
<input id="Proto.verify-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr function">
<span class="def">def</span> <span class="name">verify</span><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>
<label class="view-source-button" for="Proto.verify-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Proto.verify"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Proto.verify-102"><a href="#Proto.verify-102"><span class="linenos">102</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">verify</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
</span><span id="Proto.verify-103"><a href="#Proto.verify-103"><span class="linenos">103</span></a><span class="w"> </span><span class="sd">"""verify codes in codes file"""</span>
</span><span id="Proto.verify-104"><a href="#Proto.verify-104"><span class="linenos">104</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([])</span>
</span><span id="Proto.verify-105"><a href="#Proto.verify-105"><span class="linenos">105</span></a>
</span><span id="Proto.verify-106"><a href="#Proto.verify-106"><span class="linenos">106</span></a> <span class="c1"># Iter through each item in check.</span>
</span><span id="Proto.verify-107"><a href="#Proto.verify-107"><span class="linenos">107</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">process</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
</span><span id="Proto.verify-108"><a href="#Proto.verify-108"><span class="linenos">108</span></a> <span class="c1"># run conditional check</span>
</span><span id="Proto.verify-109"><a href="#Proto.verify-109"><span class="linenos">109</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span>
</span><span id="Proto.verify-110"><a href="#Proto.verify-110"><span class="linenos">110</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">conds</span><span class="p">,</span> <span class="n">out</span><span class="o">.</span><span class="n">all</span><span class="p">())</span>
</span><span id="Proto.verify-111"><a href="#Proto.verify-111"><span class="linenos">111</span></a>
</span><span id="Proto.verify-112"><a href="#Proto.verify-112"><span class="linenos">112</span></a> <span class="k">return</span> <span class="n">conds</span>
</span></pre></div>
<div class="docstring"><p>verify codes in codes file</p>
</div>
</div>
</section>
<section id="Read2">
<input id="Read2-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">Read2</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
<label class="view-source-button" for="Read2-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Read2"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Read2-115"><a href="#Read2-115"><span class="linenos">115</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Read2</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="Read2-116"><a href="#Read2-116"><span class="linenos">116</span></a><span class="w"> </span><span class="sd">"""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."""</span>
</span><span id="Read2-117"><a href="#Read2-117"><span class="linenos">117</span></a>
</span><span id="Read2-118"><a href="#Read2-118"><span class="linenos">118</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="Read2-119"><a href="#Read2-119"><span class="linenos">119</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"read2"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2.parquet"</span><span class="p">)</span>
</span><span id="Read2-120"><a href="#Read2-120"><span class="linenos">120</span></a>
</span><span id="Read2-121"><a href="#Read2-121"><span class="linenos">121</span></a> <span class="c1"># validate checks</span>
</span><span id="Read2-122"><a href="#Read2-122"><span class="linenos">122</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="Read2-123"><a href="#Read2-123"><span class="linenos">123</span></a> <span class="p">(</span>
</span><span id="Read2-124"><a href="#Read2-124"><span class="linenos">124</span></a> <span class="c1"># check codes are not empty, if empty throw an exception</span>
</span><span id="Read2-125"><a href="#Read2-125"><span class="linenos">125</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="Read2-126"><a href="#Read2-126"><span class="linenos">126</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="Read2-127"><a href="#Read2-127"><span class="linenos">127</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Read2-128"><a href="#Read2-128"><span class="linenos">128</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Read2-129"><a href="#Read2-129"><span class="linenos">129</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Read2-130"><a href="#Read2-130"><span class="linenos">130</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="Read2-131"><a href="#Read2-131"><span class="linenos">131</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Read2-132"><a href="#Read2-132"><span class="linenos">132</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Read2-133"><a href="#Read2-133"><span class="linenos">133</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="Read2-134"><a href="#Read2-134"><span class="linenos">134</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Read2-135"><a href="#Read2-135"><span class="linenos">135</span></a> <span class="p">)</span>
</span><span id="Read2-136"><a href="#Read2-136"><span class="linenos">136</span></a> <span class="p">)</span>
</span><span id="Read2-137"><a href="#Read2-137"><span class="linenos">137</span></a> <span class="p">),</span>
</span><span id="Read2-138"><a href="#Read2-138"><span class="linenos">138</span></a> <span class="p">),</span>
</span><span id="Read2-139"><a href="#Read2-139"><span class="linenos">139</span></a> <span class="p">(</span>
</span><span id="Read2-140"><a href="#Read2-140"><span class="linenos">140</span></a> <span class="c1"># check codes <5 characters, if too short pads it with . (dots) to reach 5 characters</span>
</span><span id="Read2-141"><a href="#Read2-141"><span class="linenos">141</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
</span><span id="Read2-142"><a href="#Read2-142"><span class="linenos">142</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">5</span><span class="p">),</span>
</span><span id="Read2-143"><a href="#Read2-143"><span class="linenos">143</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">pad</span><span class="p">(</span>
</span><span id="Read2-144"><a href="#Read2-144"><span class="linenos">144</span></a> <span class="n">width</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">side</span><span class="o">=</span><span class="s2">"right"</span><span class="p">,</span> <span class="n">fillchar</span><span class="o">=</span><span class="s2">"."</span>
</span><span id="Read2-145"><a href="#Read2-145"><span class="linenos">145</span></a> <span class="p">),</span>
</span><span id="Read2-146"><a href="#Read2-146"><span class="linenos">146</span></a> <span class="p">),</span>
</span><span id="Read2-147"><a href="#Read2-147"><span class="linenos">147</span></a> <span class="p">(</span></span><span id="Read2-148"><a href="#Read2-148"><span class="linenos">148</span></a> <span class="c1"># check codes > 5 characters, If too long, truncates them to 5 characters</span>
</span><span id="Read2-149"><a href="#Read2-149"><span class="linenos">149</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
</span><span id="Read2-150"><a href="#Read2-150"><span class="linenos">150</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">5</span><span class="p">),</span>
</span><span id="Read2-151"><a href="#Read2-151"><span class="linenos">151</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">5</span><span class="p">],</span>
</span><span id="Read2-152"><a href="#Read2-152"><span class="linenos">152</span></a> <span class="p">),</span>
</span><span id="Read2-153"><a href="#Read2-153"><span class="linenos">153</span></a> <span class="p">(</span>
</span><span id="Read2-154"><a href="#Read2-154"><span class="linenos">154</span></a> <span class="c1"># checks codes contain numbers, or dots (.), if not logs invalid code error</span>
</span><span id="Read2-155"><a href="#Read2-155"><span class="linenos">155</span></a> <span class="s2">"Alphanumeric Dot"</span><span class="p">,</span>
</span><span id="Read2-156"><a href="#Read2-156"><span class="linenos">156</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
</span><span id="Read2-157"><a href="#Read2-157"><span class="linenos">157</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Read2-158"><a href="#Read2-158"><span class="linenos">158</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Read2-159"><a href="#Read2-159"><span class="linenos">159</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Read2-160"><a href="#Read2-160"><span class="linenos">160</span></a> <span class="sa">f</span><span class="s2">"Illegal code format, not alphanumeric dot"</span><span class="p">,</span>
</span><span id="Read2-161"><a href="#Read2-161"><span class="linenos">161</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Read2-162"><a href="#Read2-162"><span class="linenos">162</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Read2-163"><a href="#Read2-163"><span class="linenos">163</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
</span><span id="Read2-164"><a href="#Read2-164"><span class="linenos">164</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Read2-165"><a href="#Read2-165"><span class="linenos">165</span></a> <span class="p">)</span>
</span><span id="Read2-166"><a href="#Read2-166"><span class="linenos">166</span></a> <span class="p">)</span>
</span><span id="Read2-167"><a href="#Read2-167"><span class="linenos">167</span></a> <span class="p">),</span>
</span><span id="Read2-168"><a href="#Read2-168"><span class="linenos">168</span></a> <span class="p">),</span>
</span><span id="Read2-169"><a href="#Read2-169"><span class="linenos">169</span></a> <span class="p">(</span>
</span><span id="Read2-170"><a href="#Read2-170"><span class="linenos">170</span></a> <span class="c1"># checks code exists in self.db (the Read2 dataset). If missing log invalid codes.</span>
</span><span id="Read2-171"><a href="#Read2-171"><span class="linenos">171</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="Read2-172"><a href="#Read2-172"><span class="linenos">172</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="Read2-173"><a href="#Read2-173"><span class="linenos">173</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Read2-174"><a href="#Read2-174"><span class="linenos">174</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Read2-175"><a href="#Read2-175"><span class="linenos">175</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Read2-176"><a href="#Read2-176"><span class="linenos">176</span></a> <span class="sa">f</span><span class="s2">"Codes do not exist in database"</span><span class="p">,</span>
</span><span id="Read2-177"><a href="#Read2-177"><span class="linenos">177</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Read2-178"><a href="#Read2-178"><span class="linenos">178</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Read2-179"><a href="#Read2-179"><span class="linenos">179</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="Read2-180"><a href="#Read2-180"><span class="linenos">180</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Read2-181"><a href="#Read2-181"><span class="linenos">181</span></a> <span class="p">)</span>
</span><span id="Read2-182"><a href="#Read2-182"><span class="linenos">182</span></a> <span class="p">)</span>
</span><span id="Read2-183"><a href="#Read2-183"><span class="linenos">183</span></a> <span class="p">),</span>
</span><span id="Read2-184"><a href="#Read2-184"><span class="linenos">184</span></a> <span class="p">),</span>
</span><span id="Read2-185"><a href="#Read2-185"><span class="linenos">185</span></a> <span class="p">]</span>
</span></pre></div>
<div class="docstring"><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>
</div>
<div id="Read2.checks" class="classattr">
<div class="attr variable">
<span class="name">checks</span>
</div>
<a class="headerlink" href="#Read2.checks"></a>
</div>
<div class="inherited">
<h5>Inherited Members</h5>
<dl>
<div><dt><a href="#Proto">Proto</a></dt>
<dd id="Read2.name" class="variable"><a href="#Proto.name">name</a></dd>
<dd id="Read2.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
<dd id="Read2.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
<dd id="Read2.process" class="function"><a href="#Proto.process">process</a></dd>
<dd id="Read2.verify" class="function"><a href="#Proto.verify">verify</a></dd>
</div>
</dl>
</div>
</section> <section id="Read3">
<input id="Read3-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">Read3</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
<label class="view-source-button" for="Read3-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Read3"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Read3-188"><a href="#Read3-188"><span class="linenos">188</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Read3</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="Read3-189"><a href="#Read3-189"><span class="linenos">189</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="Read3-190"><a href="#Read3-190"><span class="linenos">190</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"Read3"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3.parquet"</span><span class="p">)</span>
</span><span id="Read3-191"><a href="#Read3-191"><span class="linenos">191</span></a>
</span><span id="Read3-192"><a href="#Read3-192"><span class="linenos">192</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="Read3-193"><a href="#Read3-193"><span class="linenos">193</span></a> <span class="p">(</span>
</span><span id="Read3-194"><a href="#Read3-194"><span class="linenos">194</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="Read3-195"><a href="#Read3-195"><span class="linenos">195</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="Read3-196"><a href="#Read3-196"><span class="linenos">196</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Read3-197"><a href="#Read3-197"><span class="linenos">197</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Read3-198"><a href="#Read3-198"><span class="linenos">198</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Read3-199"><a href="#Read3-199"><span class="linenos">199</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="Read3-200"><a href="#Read3-200"><span class="linenos">200</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Read3-201"><a href="#Read3-201"><span class="linenos">201</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Read3-202"><a href="#Read3-202"><span class="linenos">202</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="Read3-203"><a href="#Read3-203"><span class="linenos">203</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Read3-204"><a href="#Read3-204"><span class="linenos">204</span></a> <span class="p">)</span>
</span><span id="Read3-205"><a href="#Read3-205"><span class="linenos">205</span></a> <span class="p">)</span>
</span><span id="Read3-206"><a href="#Read3-206"><span class="linenos">206</span></a> <span class="p">),</span>
</span><span id="Read3-207"><a href="#Read3-207"><span class="linenos">207</span></a> <span class="p">),</span>
</span><span id="Read3-208"><a href="#Read3-208"><span class="linenos">208</span></a> <span class="p">(</span>
</span><span id="Read3-209"><a href="#Read3-209"><span class="linenos">209</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
</span><span id="Read3-210"><a href="#Read3-210"><span class="linenos">210</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">5</span><span class="p">),</span>
</span><span id="Read3-211"><a href="#Read3-211"><span class="linenos">211</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">pad</span><span class="p">(</span>
</span><span id="Read3-212"><a href="#Read3-212"><span class="linenos">212</span></a> <span class="n">width</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">side</span><span class="o">=</span><span class="s2">"right"</span><span class="p">,</span> <span class="n">fillchar</span><span class="o">=</span><span class="s2">"."</span>
</span><span id="Read3-213"><a href="#Read3-213"><span class="linenos">213</span></a> <span class="p">),</span>
</span><span id="Read3-214"><a href="#Read3-214"><span class="linenos">214</span></a> <span class="p">),</span>
</span><span id="Read3-215"><a href="#Read3-215"><span class="linenos">215</span></a> <span class="p">(</span>
</span><span id="Read3-216"><a href="#Read3-216"><span class="linenos">216</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
</span><span id="Read3-217"><a href="#Read3-217"><span class="linenos">217</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">5</span><span class="p">),</span>
</span><span id="Read3-218"><a href="#Read3-218"><span class="linenos">218</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">5</span><span class="p">],</span>
</span><span id="Read3-219"><a href="#Read3-219"><span class="linenos">219</span></a> <span class="p">),</span>
</span><span id="Read3-220"><a href="#Read3-220"><span class="linenos">220</span></a> <span class="p">(</span>
</span><span id="Read3-221"><a href="#Read3-221"><span class="linenos">221</span></a> <span class="s2">"Alphanumeric Dot"</span><span class="p">,</span>
</span><span id="Read3-222"><a href="#Read3-222"><span class="linenos">222</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
</span><span id="Read3-223"><a href="#Read3-223"><span class="linenos">223</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Read3-224"><a href="#Read3-224"><span class="linenos">224</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Read3-225"><a href="#Read3-225"><span class="linenos">225</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Read3-226"><a href="#Read3-226"><span class="linenos">226</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Dot"</span><span class="p">,</span>
</span><span id="Read3-227"><a href="#Read3-227"><span class="linenos">227</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Read3-228"><a href="#Read3-228"><span class="linenos">228</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Read3-229"><a href="#Read3-229"><span class="linenos">229</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
</span><span id="Read3-230"><a href="#Read3-230"><span class="linenos">230</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Read3-231"><a href="#Read3-231"><span class="linenos">231</span></a> <span class="p">)</span>
</span><span id="Read3-232"><a href="#Read3-232"><span class="linenos">232</span></a> <span class="p">)</span>
</span><span id="Read3-233"><a href="#Read3-233"><span class="linenos">233</span></a> <span class="p">),</span>
</span><span id="Read3-234"><a href="#Read3-234"><span class="linenos">234</span></a> <span class="p">),</span>
</span><span id="Read3-235"><a href="#Read3-235"><span class="linenos">235</span></a> <span class="p">(</span>
</span><span id="Read3-236"><a href="#Read3-236"><span class="linenos">236</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="Read3-237"><a href="#Read3-237"><span class="linenos">237</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="Read3-238"><a href="#Read3-238"><span class="linenos">238</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Read3-239"><a href="#Read3-239"><span class="linenos">239</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Read3-240"><a href="#Read3-240"><span class="linenos">240</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Read3-241"><a href="#Read3-241"><span class="linenos">241</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
</span><span id="Read3-242"><a href="#Read3-242"><span class="linenos">242</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Read3-243"><a href="#Read3-243"><span class="linenos">243</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Read3-244"><a href="#Read3-244"><span class="linenos">244</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="Read3-245"><a href="#Read3-245"><span class="linenos">245</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Read3-246"><a href="#Read3-246"><span class="linenos">246</span></a> <span class="p">)</span></span><span id="Read3-247"><a href="#Read3-247"><span class="linenos">247</span></a> <span class="p">)</span>
</span><span id="Read3-248"><a href="#Read3-248"><span class="linenos">248</span></a> <span class="p">),</span>
</span><span id="Read3-249"><a href="#Read3-249"><span class="linenos">249</span></a> <span class="p">),</span>
</span><span id="Read3-250"><a href="#Read3-250"><span class="linenos">250</span></a> <span class="p">]</span>
</span></pre></div>
<div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
<ul>
<li>Message = The name of the condition (what is printed and logged)</li>
<li>Condition = True if Passed, and False if Failed</li>
<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
</ul>
</div>
<div id="Read3.checks" class="classattr">
<div class="attr variable">
<span class="name">checks</span>
</div>
<a class="headerlink" href="#Read3.checks"></a>
</div>
<div class="inherited">
<h5>Inherited Members</h5>
<dl>
<div><dt><a href="#Proto">Proto</a></dt>
<dd id="Read3.name" class="variable"><a href="#Proto.name">name</a></dd>
<dd id="Read3.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
<dd id="Read3.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
<dd id="Read3.process" class="function"><a href="#Proto.process">process</a></dd>
<dd id="Read3.verify" class="function"><a href="#Proto.verify">verify</a></dd>
</div>
</dl>
</div>
</section>
<section id="Icd10">
<input id="Icd10-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">Icd10</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
<label class="view-source-button" for="Icd10-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Icd10"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Icd10-253"><a href="#Icd10-253"><span class="linenos">253</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Icd10</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="Icd10-254"><a href="#Icd10-254"><span class="linenos">254</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="Icd10-255"><a href="#Icd10-255"><span class="linenos">255</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"icd10"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"icd10.parquet"</span><span class="p">)</span>
</span><span id="Icd10-256"><a href="#Icd10-256"><span class="linenos">256</span></a>
</span><span id="Icd10-257"><a href="#Icd10-257"><span class="linenos">257</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="Icd10-258"><a href="#Icd10-258"><span class="linenos">258</span></a> <span class="p">(</span>
</span><span id="Icd10-259"><a href="#Icd10-259"><span class="linenos">259</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="Icd10-260"><a href="#Icd10-260"><span class="linenos">260</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="Icd10-261"><a href="#Icd10-261"><span class="linenos">261</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Icd10-262"><a href="#Icd10-262"><span class="linenos">262</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Icd10-263"><a href="#Icd10-263"><span class="linenos">263</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Icd10-264"><a href="#Icd10-264"><span class="linenos">264</span></a> <span class="sa">f</span><span class="s2">"Code list is empty </span><span class="si">{</span><span class="n">codes_file</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
</span><span id="Icd10-265"><a href="#Icd10-265"><span class="linenos">265</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Icd10-266"><a href="#Icd10-266"><span class="linenos">266</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Icd10-267"><a href="#Icd10-267"><span class="linenos">267</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="Icd10-268"><a href="#Icd10-268"><span class="linenos">268</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Icd10-269"><a href="#Icd10-269"><span class="linenos">269</span></a> <span class="p">)</span></span><span id="Icd10-270"><a href="#Icd10-270"><span class="linenos">270</span></a> <span class="p">)</span>
</span><span id="Icd10-271"><a href="#Icd10-271"><span class="linenos">271</span></a> <span class="p">),</span>
</span><span id="Icd10-272"><a href="#Icd10-272"><span class="linenos">272</span></a> <span class="p">),</span>
</span><span id="Icd10-273"><a href="#Icd10-273"><span class="linenos">273</span></a> <span class="p">(</span>
</span><span id="Icd10-274"><a href="#Icd10-274"><span class="linenos">274</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
</span><span id="Icd10-275"><a href="#Icd10-275"><span class="linenos">275</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">3</span><span class="p">),</span>
</span><span id="Icd10-276"><a href="#Icd10-276"><span class="linenos">276</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Icd10-277"><a href="#Icd10-277"><span class="linenos">277</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Icd10-278"><a href="#Icd10-278"><span class="linenos">278</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Icd10-279"><a href="#Icd10-279"><span class="linenos">279</span></a> <span class="sa">f</span><span class="s2">"QA Too Short"</span><span class="p">,</span>
</span><span id="Icd10-280"><a href="#Icd10-280"><span class="linenos">280</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Icd10-281"><a href="#Icd10-281"><span class="linenos">281</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Icd10-282"><a href="#Icd10-282"><span class="linenos">282</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">3</span><span class="p">),</span>
</span><span id="Icd10-283"><a href="#Icd10-283"><span class="linenos">283</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Icd10-284"><a href="#Icd10-284"><span class="linenos">284</span></a> <span class="p">)</span>
</span><span id="Icd10-285"><a href="#Icd10-285"><span class="linenos">285</span></a> <span class="p">)</span>
</span><span id="Icd10-286"><a href="#Icd10-286"><span class="linenos">286</span></a> <span class="p">),</span>
</span><span id="Icd10-287"><a href="#Icd10-287"><span class="linenos">287</span></a> <span class="p">),</span>
</span><span id="Icd10-288"><a href="#Icd10-288"><span class="linenos">288</span></a> <span class="p">(</span>
</span><span id="Icd10-289"><a href="#Icd10-289"><span class="linenos">289</span></a> <span class="s2">"Has Dot"</span><span class="p">,</span>
</span><span id="Icd10-290"><a href="#Icd10-290"><span class="linenos">290</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">".*\..*"</span><span class="p">)),</span> <span class="c1"># check if contains dot</span>
</span><span id="Icd10-291"><a href="#Icd10-291"><span class="linenos">291</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
</span><span id="Icd10-292"><a href="#Icd10-292"><span class="linenos">292</span></a> <span class="s2">"."</span><span class="p">,</span> <span class="s2">""</span>
</span><span id="Icd10-293"><a href="#Icd10-293"><span class="linenos">293</span></a> <span class="p">),</span> <span class="c1"># delete any dots in string</span>
</span><span id="Icd10-294"><a href="#Icd10-294"><span class="linenos">294</span></a> <span class="c1"># lambda codes : codes.str.split('\.').apply(lambda ls: ls[0]) #only get part before dot</span>
</span><span id="Icd10-295"><a href="#Icd10-295"><span class="linenos">295</span></a> <span class="p">),</span>
</span><span id="Icd10-296"><a href="#Icd10-296"><span class="linenos">296</span></a> <span class="p">(</span>
</span><span id="Icd10-297"><a href="#Icd10-297"><span class="linenos">297</span></a> <span class="s2">"Alphanumeric Capital"</span><span class="p">,</span>
</span><span id="Icd10-298"><a href="#Icd10-298"><span class="linenos">298</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
</span><span id="Icd10-299"><a href="#Icd10-299"><span class="linenos">299</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Icd10-300"><a href="#Icd10-300"><span class="linenos">300</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Icd10-301"><a href="#Icd10-301"><span class="linenos">301</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Icd10-302"><a href="#Icd10-302"><span class="linenos">302</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Capital"</span><span class="p">,</span>
</span><span id="Icd10-303"><a href="#Icd10-303"><span class="linenos">303</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Icd10-304"><a href="#Icd10-304"><span class="linenos">304</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Icd10-305"><a href="#Icd10-305"><span class="linenos">305</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
</span><span id="Icd10-306"><a href="#Icd10-306"><span class="linenos">306</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Icd10-307"><a href="#Icd10-307"><span class="linenos">307</span></a> <span class="p">)</span>
</span><span id="Icd10-308"><a href="#Icd10-308"><span class="linenos">308</span></a> <span class="p">)</span>
</span><span id="Icd10-309"><a href="#Icd10-309"><span class="linenos">309</span></a> <span class="p">),</span>
</span><span id="Icd10-310"><a href="#Icd10-310"><span class="linenos">310</span></a> <span class="p">),</span>
</span><span id="Icd10-311"><a href="#Icd10-311"><span class="linenos">311</span></a> <span class="p">(</span>
</span><span id="Icd10-312"><a href="#Icd10-312"><span class="linenos">312</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="Icd10-313"><a href="#Icd10-313"><span class="linenos">313</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span>
</span><span id="Icd10-314"><a href="#Icd10-314"><span class="linenos">314</span></a> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
</span><span id="Icd10-315"><a href="#Icd10-315"><span class="linenos">315</span></a> <span class="o">&</span> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s2">"_alt"</span><span class="p">)</span>
</span><span id="Icd10-316"><a href="#Icd10-316"><span class="linenos">316</span></a> <span class="p">),</span>
</span><span id="Icd10-317"><a href="#Icd10-317"><span class="linenos">317</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Icd10-318"><a href="#Icd10-318"><span class="linenos">318</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Icd10-319"><a href="#Icd10-319"><span class="linenos">319</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Icd10-320"><a href="#Icd10-320"><span class="linenos">320</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
</span><span id="Icd10-321"><a href="#Icd10-321"><span class="linenos">321</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Icd10-322"><a href="#Icd10-322"><span class="linenos">322</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Icd10-323"><a href="#Icd10-323"><span class="linenos">323</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span>
</span><span id="Icd10-324"><a href="#Icd10-324"><span class="linenos">324</span></a> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
</span><span id="Icd10-325"><a href="#Icd10-325"><span class="linenos">325</span></a> <span class="o">&</span> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s2">"_alt"</span><span class="p">)</span>
</span><span id="Icd10-326"><a href="#Icd10-326"><span class="linenos">326</span></a> <span class="p">),</span>
</span><span id="Icd10-327"><a href="#Icd10-327"><span class="linenos">327</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Icd10-328"><a href="#Icd10-328"><span class="linenos">328</span></a> <span class="p">)</span>
</span><span id="Icd10-329"><a href="#Icd10-329"><span class="linenos">329</span></a> <span class="p">)</span>
</span><span id="Icd10-330"><a href="#Icd10-330"><span class="linenos">330</span></a> <span class="p">),</span>
</span><span id="Icd10-331"><a href="#Icd10-331"><span class="linenos">331</span></a> <span class="p">),</span>
</span><span id="Icd10-332"><a href="#Icd10-332"><span class="linenos">332</span></a> <span class="c1"># (</span>
</span><span id="Icd10-333"><a href="#Icd10-333"><span class="linenos">333</span></a> <span class="c1"># "ICD10 Regex",</span>
</span><span id="Icd10-334"><a href="#Icd10-334"><span class="linenos">334</span></a> <span class="c1"># lambda codes : codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Alpha, Num, Num , Dot?, 4xAlphNum*</span>
</span><span id="Icd10-335"><a href="#Icd10-335"><span class="linenos">335</span></a> <span class="c1"># lambda codes : lc.log_invalid_code(codes,</span>
</span><span id="Icd10-336"><a href="#Icd10-336"><span class="linenos">336</span></a> <span class="c1"># codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Log non-matching rows</span>
</span><span id="Icd10-337"><a href="#Icd10-337"><span class="linenos">337</span></a> <span class="c1"># code_type="icd10",</span>
</span><span id="Icd10-338"><a href="#Icd10-338"><span class="linenos">338</span></a> <span class="c1">#</span>
</span><span id="Icd10-339"><a href="#Icd10-339"><span class="linenos">339</span></a> <span class="c1"># )</span></span><span id="Icd10-340"><a href="#Icd10-340"><span class="linenos">340</span></a> <span class="p">]</span>
</span></pre></div>
<div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
<ul>
<li>Message = The name of the condition (what is printed and logged)</li>
<li>Condition = True if Passed, and False if Failed</li>
<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
</ul>
</div>
<div id="Icd10.checks" class="classattr">
<div class="attr variable">
<span class="name">checks</span>
</div>
<a class="headerlink" href="#Icd10.checks"></a>
</div>
<div class="inherited">
<h5>Inherited Members</h5>
<dl>
<div><dt><a href="#Proto">Proto</a></dt>
<dd id="Icd10.name" class="variable"><a href="#Proto.name">name</a></dd>
<dd id="Icd10.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
<dd id="Icd10.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
<dd id="Icd10.process" class="function"><a href="#Proto.process">process</a></dd>
<dd id="Icd10.verify" class="function"><a href="#Proto.verify">verify</a></dd>
</div>
</dl>
</div>
</section>
<section id="Snomed">
<input id="Snomed-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">Snomed</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
<label class="view-source-button" for="Snomed-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Snomed"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Snomed-343"><a href="#Snomed-343"><span class="linenos">343</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Snomed</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="Snomed-344"><a href="#Snomed-344"><span class="linenos">344</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="Snomed-345"><a href="#Snomed-345"><span class="linenos">345</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"snomed"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"snomed.parquet"</span><span class="p">)</span>
</span><span id="Snomed-346"><a href="#Snomed-346"><span class="linenos">346</span></a>
</span><span id="Snomed-347"><a href="#Snomed-347"><span class="linenos">347</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="Snomed-348"><a href="#Snomed-348"><span class="linenos">348</span></a> <span class="c1"># (</span>
</span><span id="Snomed-349"><a href="#Snomed-349"><span class="linenos">349</span></a> <span class="c1"># "Not Empty",</span>
</span><span id="Snomed-350"><a href="#Snomed-350"><span class="linenos">350</span></a> <span class="c1"># lambda codes : pd.Series([len(codes) > 0]),</span>
</span><span id="Snomed-351"><a href="#Snomed-351"><span class="linenos">351</span></a> <span class="c1"># lambda codes : raise_exception(Exception("Code List is Empty"))</span>
</span><span id="Snomed-352"><a href="#Snomed-352"><span class="linenos">352</span></a> <span class="c1"># ),</span>
</span><span id="Snomed-353"><a href="#Snomed-353"><span class="linenos">353</span></a> <span class="p">(</span>
</span><span id="Snomed-354"><a href="#Snomed-354"><span class="linenos">354</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
</span><span id="Snomed-355"><a href="#Snomed-355"><span class="linenos">355</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">6</span><span class="p">),</span>
</span><span id="Snomed-356"><a href="#Snomed-356"><span class="linenos">356</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Snomed-357"><a href="#Snomed-357"><span class="linenos">357</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Snomed-358"><a href="#Snomed-358"><span class="linenos">358</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Snomed-359"><a href="#Snomed-359"><span class="linenos">359</span></a> <span class="sa">f</span><span class="s2">"QA Too Short"</span><span class="p">,</span>
</span><span id="Snomed-360"><a href="#Snomed-360"><span class="linenos">360</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Snomed-361"><a href="#Snomed-361"><span class="linenos">361</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Snomed-362"><a href="#Snomed-362"><span class="linenos">362</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">6</span><span class="p">),</span></span><span id="Snomed-363"><a href="#Snomed-363"><span class="linenos">363</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Snomed-364"><a href="#Snomed-364"><span class="linenos">364</span></a> <span class="p">)</span>
</span><span id="Snomed-365"><a href="#Snomed-365"><span class="linenos">365</span></a> <span class="p">)</span>
</span><span id="Snomed-366"><a href="#Snomed-366"><span class="linenos">366</span></a> <span class="p">),</span>
</span><span id="Snomed-367"><a href="#Snomed-367"><span class="linenos">367</span></a> <span class="p">),</span>
</span><span id="Snomed-368"><a href="#Snomed-368"><span class="linenos">368</span></a> <span class="p">(</span>
</span><span id="Snomed-369"><a href="#Snomed-369"><span class="linenos">369</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
</span><span id="Snomed-370"><a href="#Snomed-370"><span class="linenos">370</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">18</span><span class="p">),</span>
</span><span id="Snomed-371"><a href="#Snomed-371"><span class="linenos">371</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Snomed-372"><a href="#Snomed-372"><span class="linenos">372</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Snomed-373"><a href="#Snomed-373"><span class="linenos">373</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Snomed-374"><a href="#Snomed-374"><span class="linenos">374</span></a> <span class="sa">f</span><span class="s2">"QA Too Long"</span><span class="p">,</span>
</span><span id="Snomed-375"><a href="#Snomed-375"><span class="linenos">375</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Snomed-376"><a href="#Snomed-376"><span class="linenos">376</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Snomed-377"><a href="#Snomed-377"><span class="linenos">377</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">18</span><span class="p">),</span>
</span><span id="Snomed-378"><a href="#Snomed-378"><span class="linenos">378</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Snomed-379"><a href="#Snomed-379"><span class="linenos">379</span></a> <span class="p">)</span>
</span><span id="Snomed-380"><a href="#Snomed-380"><span class="linenos">380</span></a> <span class="p">)</span>
</span><span id="Snomed-381"><a href="#Snomed-381"><span class="linenos">381</span></a> <span class="p">),</span>
</span><span id="Snomed-382"><a href="#Snomed-382"><span class="linenos">382</span></a> <span class="p">),</span>
</span><span id="Snomed-383"><a href="#Snomed-383"><span class="linenos">383</span></a> <span class="p">(</span>
</span><span id="Snomed-384"><a href="#Snomed-384"><span class="linenos">384</span></a> <span class="s2">"Numeric"</span><span class="p">,</span>
</span><span id="Snomed-385"><a href="#Snomed-385"><span class="linenos">385</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[0-9]+$"</span><span class="p">),</span>
</span><span id="Snomed-386"><a href="#Snomed-386"><span class="linenos">386</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Snomed-387"><a href="#Snomed-387"><span class="linenos">387</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Snomed-388"><a href="#Snomed-388"><span class="linenos">388</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Snomed-389"><a href="#Snomed-389"><span class="linenos">389</span></a> <span class="sa">f</span><span class="s2">"QA Numeric"</span><span class="p">,</span>
</span><span id="Snomed-390"><a href="#Snomed-390"><span class="linenos">390</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Snomed-391"><a href="#Snomed-391"><span class="linenos">391</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Snomed-392"><a href="#Snomed-392"><span class="linenos">392</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[0-9]+$"</span><span class="p">),</span>
</span><span id="Snomed-393"><a href="#Snomed-393"><span class="linenos">393</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Snomed-394"><a href="#Snomed-394"><span class="linenos">394</span></a> <span class="p">)</span>
</span><span id="Snomed-395"><a href="#Snomed-395"><span class="linenos">395</span></a> <span class="p">)</span>
</span><span id="Snomed-396"><a href="#Snomed-396"><span class="linenos">396</span></a> <span class="p">),</span>
</span><span id="Snomed-397"><a href="#Snomed-397"><span class="linenos">397</span></a> <span class="p">),</span>
</span><span id="Snomed-398"><a href="#Snomed-398"><span class="linenos">398</span></a> <span class="c1"># (</span>
</span><span id="Snomed-399"><a href="#Snomed-399"><span class="linenos">399</span></a> <span class="c1"># "Is Integer",</span>
</span><span id="Snomed-400"><a href="#Snomed-400"><span class="linenos">400</span></a> <span class="c1"># lambda codes : codes.dtype == int,</span>
</span><span id="Snomed-401"><a href="#Snomed-401"><span class="linenos">401</span></a> <span class="c1"># lambda codes : codes.astype(int) #Convert to integer</span>
</span><span id="Snomed-402"><a href="#Snomed-402"><span class="linenos">402</span></a> <span class="c1"># ),</span>
</span><span id="Snomed-403"><a href="#Snomed-403"><span class="linenos">403</span></a> <span class="p">(</span>
</span><span id="Snomed-404"><a href="#Snomed-404"><span class="linenos">404</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="Snomed-405"><a href="#Snomed-405"><span class="linenos">405</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="Snomed-406"><a href="#Snomed-406"><span class="linenos">406</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Snomed-407"><a href="#Snomed-407"><span class="linenos">407</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Snomed-408"><a href="#Snomed-408"><span class="linenos">408</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Snomed-409"><a href="#Snomed-409"><span class="linenos">409</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
</span><span id="Snomed-410"><a href="#Snomed-410"><span class="linenos">410</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Snomed-411"><a href="#Snomed-411"><span class="linenos">411</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Snomed-412"><a href="#Snomed-412"><span class="linenos">412</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="Snomed-413"><a href="#Snomed-413"><span class="linenos">413</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Snomed-414"><a href="#Snomed-414"><span class="linenos">414</span></a> <span class="p">)</span>
</span><span id="Snomed-415"><a href="#Snomed-415"><span class="linenos">415</span></a> <span class="p">)</span>
</span><span id="Snomed-416"><a href="#Snomed-416"><span class="linenos">416</span></a> <span class="p">),</span>
</span><span id="Snomed-417"><a href="#Snomed-417"><span class="linenos">417</span></a> <span class="p">),</span>
</span><span id="Snomed-418"><a href="#Snomed-418"><span class="linenos">418</span></a> <span class="p">]</span>
</span></pre></div>
<div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
<ul>
<li>Message = The name of the condition (what is printed and logged)</li>
<li>Condition = True if Passed, and False if Failed</li>
<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
</ul>
</div>
<div id="Snomed.checks" class="classattr"> <div class="attr variable">
<span class="name">checks</span>
</div>
<a class="headerlink" href="#Snomed.checks"></a>
</div>
<div class="inherited">
<h5>Inherited Members</h5>
<dl>
<div><dt><a href="#Proto">Proto</a></dt>
<dd id="Snomed.name" class="variable"><a href="#Proto.name">name</a></dd>
<dd id="Snomed.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
<dd id="Snomed.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
<dd id="Snomed.process" class="function"><a href="#Proto.process">process</a></dd>
<dd id="Snomed.verify" class="function"><a href="#Proto.verify">verify</a></dd>
</div>
</dl>
</div>
</section>
<section id="Opcs4">
<input id="Opcs4-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">Opcs4</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
<label class="view-source-button" for="Opcs4-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Opcs4"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Opcs4-421"><a href="#Opcs4-421"><span class="linenos">421</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Opcs4</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="Opcs4-422"><a href="#Opcs4-422"><span class="linenos">422</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="Opcs4-423"><a href="#Opcs4-423"><span class="linenos">423</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"opcs4"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"opcs4.parquet"</span><span class="p">)</span>
</span><span id="Opcs4-424"><a href="#Opcs4-424"><span class="linenos">424</span></a>
</span><span id="Opcs4-425"><a href="#Opcs4-425"><span class="linenos">425</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="Opcs4-426"><a href="#Opcs4-426"><span class="linenos">426</span></a> <span class="p">(</span>
</span><span id="Opcs4-427"><a href="#Opcs4-427"><span class="linenos">427</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="Opcs4-428"><a href="#Opcs4-428"><span class="linenos">428</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="Opcs4-429"><a href="#Opcs4-429"><span class="linenos">429</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Opcs4-430"><a href="#Opcs4-430"><span class="linenos">430</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Opcs4-431"><a href="#Opcs4-431"><span class="linenos">431</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Opcs4-432"><a href="#Opcs4-432"><span class="linenos">432</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="Opcs4-433"><a href="#Opcs4-433"><span class="linenos">433</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Opcs4-434"><a href="#Opcs4-434"><span class="linenos">434</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Opcs4-435"><a href="#Opcs4-435"><span class="linenos">435</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="Opcs4-436"><a href="#Opcs4-436"><span class="linenos">436</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Opcs4-437"><a href="#Opcs4-437"><span class="linenos">437</span></a> <span class="p">)</span>
</span><span id="Opcs4-438"><a href="#Opcs4-438"><span class="linenos">438</span></a> <span class="p">)</span>
</span><span id="Opcs4-439"><a href="#Opcs4-439"><span class="linenos">439</span></a> <span class="p">),</span>
</span><span id="Opcs4-440"><a href="#Opcs4-440"><span class="linenos">440</span></a> <span class="p">),</span>
</span><span id="Opcs4-441"><a href="#Opcs4-441"><span class="linenos">441</span></a> <span class="p">(</span>
</span><span id="Opcs4-442"><a href="#Opcs4-442"><span class="linenos">442</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
</span><span id="Opcs4-443"><a href="#Opcs4-443"><span class="linenos">443</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="Opcs4-444"><a href="#Opcs4-444"><span class="linenos">444</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Opcs4-445"><a href="#Opcs4-445"><span class="linenos">445</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Opcs4-446"><a href="#Opcs4-446"><span class="linenos">446</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Opcs4-447"><a href="#Opcs4-447"><span class="linenos">447</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
</span><span id="Opcs4-448"><a href="#Opcs4-448"><span class="linenos">448</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Opcs4-449"><a href="#Opcs4-449"><span class="linenos">449</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Opcs4-450"><a href="#Opcs4-450"><span class="linenos">450</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
</span><span id="Opcs4-451"><a href="#Opcs4-451"><span class="linenos">451</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Opcs4-452"><a href="#Opcs4-452"><span class="linenos">452</span></a> <span class="p">)</span>
</span><span id="Opcs4-453"><a href="#Opcs4-453"><span class="linenos">453</span></a> <span class="p">)</span>
</span><span id="Opcs4-454"><a href="#Opcs4-454"><span class="linenos">454</span></a> <span class="p">),</span>
</span><span id="Opcs4-455"><a href="#Opcs4-455"><span class="linenos">455</span></a> <span class="p">),</span></span><span id="Opcs4-456"><a href="#Opcs4-456"><span class="linenos">456</span></a> <span class="p">]</span>
</span></pre></div>
<div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
<ul>
<li>Message = The name of the condition (what is printed and logged)</li>
<li>Condition = True if Passed, and False if Failed</li>
<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
</ul>
</div>
<div id="Opcs4.checks" class="classattr">
<div class="attr variable">
<span class="name">checks</span>
</div>
<a class="headerlink" href="#Opcs4.checks"></a>
</div>
<div class="inherited">
<h5>Inherited Members</h5>
<dl>
<div><dt><a href="#Proto">Proto</a></dt>
<dd id="Opcs4.name" class="variable"><a href="#Proto.name">name</a></dd>
<dd id="Opcs4.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
<dd id="Opcs4.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
<dd id="Opcs4.process" class="function"><a href="#Proto.process">process</a></dd>
<dd id="Opcs4.verify" class="function"><a href="#Proto.verify">verify</a></dd>
</div>
</dl>
</div>
</section>
<section id="Atc">
<input id="Atc-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">Atc</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
<label class="view-source-button" for="Atc-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Atc"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Atc-459"><a href="#Atc-459"><span class="linenos">459</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Atc</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="Atc-460"><a href="#Atc-460"><span class="linenos">460</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="Atc-461"><a href="#Atc-461"><span class="linenos">461</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"atc"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
</span><span id="Atc-462"><a href="#Atc-462"><span class="linenos">462</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="Atc-463"><a href="#Atc-463"><span class="linenos">463</span></a> <span class="p">(</span>
</span><span id="Atc-464"><a href="#Atc-464"><span class="linenos">464</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="Atc-465"><a href="#Atc-465"><span class="linenos">465</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="Atc-466"><a href="#Atc-466"><span class="linenos">466</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Atc-467"><a href="#Atc-467"><span class="linenos">467</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Atc-468"><a href="#Atc-468"><span class="linenos">468</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Atc-469"><a href="#Atc-469"><span class="linenos">469</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="Atc-470"><a href="#Atc-470"><span class="linenos">470</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Atc-471"><a href="#Atc-471"><span class="linenos">471</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Atc-472"><a href="#Atc-472"><span class="linenos">472</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="Atc-473"><a href="#Atc-473"><span class="linenos">473</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Atc-474"><a href="#Atc-474"><span class="linenos">474</span></a> <span class="p">)</span>
</span><span id="Atc-475"><a href="#Atc-475"><span class="linenos">475</span></a> <span class="p">)</span>
</span><span id="Atc-476"><a href="#Atc-476"><span class="linenos">476</span></a> <span class="p">),</span>
</span><span id="Atc-477"><a href="#Atc-477"><span class="linenos">477</span></a> <span class="p">),</span>
</span><span id="Atc-478"><a href="#Atc-478"><span class="linenos">478</span></a> <span class="p">(</span></span><span id="Atc-479"><a href="#Atc-479"><span class="linenos">479</span></a> <span class="s2">"Alphanumeric Capital"</span><span class="p">,</span>
</span><span id="Atc-480"><a href="#Atc-480"><span class="linenos">480</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
</span><span id="Atc-481"><a href="#Atc-481"><span class="linenos">481</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Atc-482"><a href="#Atc-482"><span class="linenos">482</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Atc-483"><a href="#Atc-483"><span class="linenos">483</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Atc-484"><a href="#Atc-484"><span class="linenos">484</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Capital"</span><span class="p">,</span>
</span><span id="Atc-485"><a href="#Atc-485"><span class="linenos">485</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Atc-486"><a href="#Atc-486"><span class="linenos">486</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Atc-487"><a href="#Atc-487"><span class="linenos">487</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
</span><span id="Atc-488"><a href="#Atc-488"><span class="linenos">488</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Atc-489"><a href="#Atc-489"><span class="linenos">489</span></a> <span class="p">)</span>
</span><span id="Atc-490"><a href="#Atc-490"><span class="linenos">490</span></a> <span class="p">)</span>
</span><span id="Atc-491"><a href="#Atc-491"><span class="linenos">491</span></a> <span class="p">),</span>
</span><span id="Atc-492"><a href="#Atc-492"><span class="linenos">492</span></a> <span class="p">),</span>
</span><span id="Atc-493"><a href="#Atc-493"><span class="linenos">493</span></a> <span class="p">]</span>
</span></pre></div>
<div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
<ul>
<li>Message = The name of the condition (what is printed and logged)</li>
<li>Condition = True if Passed, and False if Failed</li>
<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
</ul>
</div>
<div id="Atc.checks" class="classattr">
<div class="attr variable">
<span class="name">checks</span>
</div>
<a class="headerlink" href="#Atc.checks"></a>
</div>
<div class="inherited">
<h5>Inherited Members</h5>
<dl>
<div><dt><a href="#Proto">Proto</a></dt>
<dd id="Atc.name" class="variable"><a href="#Proto.name">name</a></dd>
<dd id="Atc.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
<dd id="Atc.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
<dd id="Atc.process" class="function"><a href="#Proto.process">process</a></dd>
<dd id="Atc.verify" class="function"><a href="#Proto.verify">verify</a></dd>
</div>
</dl>
</div>
</section>
<section id="Med">
<input id="Med-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">Med</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
<label class="view-source-button" for="Med-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Med"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Med-496"><a href="#Med-496"><span class="linenos">496</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Med</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="Med-497"><a href="#Med-497"><span class="linenos">497</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="Med-498"><a href="#Med-498"><span class="linenos">498</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"med"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
</span><span id="Med-499"><a href="#Med-499"><span class="linenos">499</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="Med-500"><a href="#Med-500"><span class="linenos">500</span></a> <span class="p">(</span>
</span><span id="Med-501"><a href="#Med-501"><span class="linenos">501</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span></span><span id="Med-502"><a href="#Med-502"><span class="linenos">502</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
</span><span id="Med-503"><a href="#Med-503"><span class="linenos">503</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Med-504"><a href="#Med-504"><span class="linenos">504</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Med-505"><a href="#Med-505"><span class="linenos">505</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Med-506"><a href="#Med-506"><span class="linenos">506</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="Med-507"><a href="#Med-507"><span class="linenos">507</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Med-508"><a href="#Med-508"><span class="linenos">508</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Med-509"><a href="#Med-509"><span class="linenos">509</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="Med-510"><a href="#Med-510"><span class="linenos">510</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Med-511"><a href="#Med-511"><span class="linenos">511</span></a> <span class="p">)</span>
</span><span id="Med-512"><a href="#Med-512"><span class="linenos">512</span></a> <span class="p">)</span>
</span><span id="Med-513"><a href="#Med-513"><span class="linenos">513</span></a> <span class="p">),</span>
</span><span id="Med-514"><a href="#Med-514"><span class="linenos">514</span></a> <span class="p">)</span>
</span><span id="Med-515"><a href="#Med-515"><span class="linenos">515</span></a> <span class="p">]</span>
</span></pre></div>
<div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
<ul>
<li>Message = The name of the condition (what is printed and logged)</li>
<li>Condition = True if Passed, and False if Failed</li>
<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
</ul>
</div>
<div id="Med.checks" class="classattr">
<div class="attr variable">
<span class="name">checks</span>
</div>
<a class="headerlink" href="#Med.checks"></a>
</div>
<div class="inherited">
<h5>Inherited Members</h5>
<dl>
<div><dt><a href="#Proto">Proto</a></dt>
<dd id="Med.name" class="variable"><a href="#Proto.name">name</a></dd>
<dd id="Med.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
<dd id="Med.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
<dd id="Med.process" class="function"><a href="#Proto.process">process</a></dd>
<dd id="Med.verify" class="function"><a href="#Proto.verify">verify</a></dd>
</div>
</dl>
</div>
</section>
<section id="Cprd">
<input id="Cprd-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">Cprd</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
<label class="view-source-button" for="Cprd-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#Cprd"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="Cprd-518"><a href="#Cprd-518"><span class="linenos">518</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Cprd</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
</span><span id="Cprd-519"><a href="#Cprd-519"><span class="linenos">519</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
</span><span id="Cprd-520"><a href="#Cprd-520"><span class="linenos">520</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"cprd"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
</span><span id="Cprd-521"><a href="#Cprd-521"><span class="linenos">521</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
</span><span id="Cprd-522"><a href="#Cprd-522"><span class="linenos">522</span></a> <span class="p">(</span>
</span><span id="Cprd-523"><a href="#Cprd-523"><span class="linenos">523</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
</span><span id="Cprd-524"><a href="#Cprd-524"><span class="linenos">524</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span></span><span id="Cprd-525"><a href="#Cprd-525"><span class="linenos">525</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
</span><span id="Cprd-526"><a href="#Cprd-526"><span class="linenos">526</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
</span><span id="Cprd-527"><a href="#Cprd-527"><span class="linenos">527</span></a> <span class="n">CodesError</span><span class="p">(</span>
</span><span id="Cprd-528"><a href="#Cprd-528"><span class="linenos">528</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
</span><span id="Cprd-529"><a href="#Cprd-529"><span class="linenos">529</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
</span><span id="Cprd-530"><a href="#Cprd-530"><span class="linenos">530</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
</span><span id="Cprd-531"><a href="#Cprd-531"><span class="linenos">531</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
</span><span id="Cprd-532"><a href="#Cprd-532"><span class="linenos">532</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
</span><span id="Cprd-533"><a href="#Cprd-533"><span class="linenos">533</span></a> <span class="p">)</span>
</span><span id="Cprd-534"><a href="#Cprd-534"><span class="linenos">534</span></a> <span class="p">)</span>
</span><span id="Cprd-535"><a href="#Cprd-535"><span class="linenos">535</span></a> <span class="p">),</span>
</span><span id="Cprd-536"><a href="#Cprd-536"><span class="linenos">536</span></a> <span class="p">)</span>
</span><span id="Cprd-537"><a href="#Cprd-537"><span class="linenos">537</span></a> <span class="p">]</span>
</span></pre></div>
<div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
<ul>
<li>Message = The name of the condition (what is printed and logged)</li>
<li>Condition = True if Passed, and False if Failed</li>
<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
</ul>
</div>
<div id="Cprd.checks" class="classattr">
<div class="attr variable">
<span class="name">checks</span>
</div>
<a class="headerlink" href="#Cprd.checks"></a>
</div>
<div class="inherited">
<h5>Inherited Members</h5>
<dl>
<div><dt><a href="#Proto">Proto</a></dt>
<dd id="Cprd.name" class="variable"><a href="#Proto.name">name</a></dd>
<dd id="Cprd.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
<dd id="Cprd.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
<dd id="Cprd.process" class="function"><a href="#Proto.process">process</a></dd>
<dd id="Cprd.verify" class="function"><a href="#Proto.verify">verify</a></dd>
</div>
</dl>
</div>
</section>
<section id="CodeTypeParser">
<input id="CodeTypeParser-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr class">
<span class="def">class</span>
<span class="name">CodeTypeParser</span>:
<label class="view-source-button" for="CodeTypeParser-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#CodeTypeParser"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="CodeTypeParser-540"><a href="#CodeTypeParser-540"><span class="linenos">540</span></a><span class="k">class</span><span class="w"> </span><span class="nc">CodeTypeParser</span><span class="p">:</span>
</span><span id="CodeTypeParser-541"><a href="#CodeTypeParser-541"><span class="linenos">541</span></a><span class="w"> </span><span class="sd">"""A class used in InvalidCodesException to report an error if a code parser check fails"""</span>
</span><span id="CodeTypeParser-542"><a href="#CodeTypeParser-542"><span class="linenos">542</span></a>
</span><span id="CodeTypeParser-543"><a href="#CodeTypeParser-543"><span class="linenos">543</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trud_processed_dir</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span><span class="p">):</span>
</span><span id="CodeTypeParser-544"><a href="#CodeTypeParser-544"><span class="linenos">544</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
</span><span id="CodeTypeParser-545"><a href="#CodeTypeParser-545"><span class="linenos">545</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
</span><span id="CodeTypeParser-546"><a href="#CodeTypeParser-546"><span class="linenos">546</span></a> <span class="sa">f</span><span class="s2">"Cannot initialise parsers as the TRUD processed directory </span><span class="si">{</span><span class="n">trud_processed_dir</span><span class="si">}</span><span class="s2"> does not exist, please check that TRUD has been installed: acmc trud install"</span>
</span><span id="CodeTypeParser-547"><a href="#CodeTypeParser-547"><span class="linenos">547</span></a> <span class="p">)</span></span><span id="CodeTypeParser-548"><a href="#CodeTypeParser-548"><span class="linenos">548</span></a>
</span><span id="CodeTypeParser-549"><a href="#CodeTypeParser-549"><span class="linenos">549</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">code_types</span> <span class="o">=</span> <span class="p">{</span>
</span><span id="CodeTypeParser-550"><a href="#CodeTypeParser-550"><span class="linenos">550</span></a> <span class="s2">"read2"</span><span class="p">:</span> <span class="n">Read2</span><span class="p">(),</span>
</span><span id="CodeTypeParser-551"><a href="#CodeTypeParser-551"><span class="linenos">551</span></a> <span class="s2">"read3"</span><span class="p">:</span> <span class="n">Read3</span><span class="p">(),</span>
</span><span id="CodeTypeParser-552"><a href="#CodeTypeParser-552"><span class="linenos">552</span></a> <span class="s2">"icd10"</span><span class="p">:</span> <span class="n">Icd10</span><span class="p">(),</span>
</span><span id="CodeTypeParser-553"><a href="#CodeTypeParser-553"><span class="linenos">553</span></a> <span class="s2">"snomed"</span><span class="p">:</span> <span class="n">Snomed</span><span class="p">(),</span>
</span><span id="CodeTypeParser-554"><a href="#CodeTypeParser-554"><span class="linenos">554</span></a> <span class="s2">"opcs4"</span><span class="p">:</span> <span class="n">Opcs4</span><span class="p">(),</span>
</span><span id="CodeTypeParser-555"><a href="#CodeTypeParser-555"><span class="linenos">555</span></a> <span class="s2">"atc"</span><span class="p">:</span> <span class="n">Atc</span><span class="p">(),</span>
</span><span id="CodeTypeParser-556"><a href="#CodeTypeParser-556"><span class="linenos">556</span></a> <span class="s2">"med"</span><span class="p">:</span> <span class="n">Med</span><span class="p">(),</span>
</span><span id="CodeTypeParser-557"><a href="#CodeTypeParser-557"><span class="linenos">557</span></a> <span class="s2">"cprd"</span><span class="p">:</span> <span class="n">Cprd</span><span class="p">(),</span>
</span><span id="CodeTypeParser-558"><a href="#CodeTypeParser-558"><span class="linenos">558</span></a> <span class="p">}</span>
</span></pre></div>
<div class="docstring"><p>A class used in InvalidCodesException to report an error if a code parser check fails</p>
</div>
<div id="CodeTypeParser.__init__" class="classattr">
<input id="CodeTypeParser.__init__-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
<div class="attr function">
<span class="name">CodeTypeParser</span><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">'vocab/trud/processed'</span><span class="p">)</span></span>)</span>
<label class="view-source-button" for="CodeTypeParser.__init__-view-source"><span>View Source</span></label>
</div>
<a class="headerlink" href="#CodeTypeParser.__init__"></a>
<div class="pdoc-code codehilite"><pre><span></span><span id="CodeTypeParser.__init__-543"><a href="#CodeTypeParser.__init__-543"><span class="linenos">543</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trud_processed_dir</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span><span class="p">):</span>
</span><span id="CodeTypeParser.__init__-544"><a href="#CodeTypeParser.__init__-544"><span class="linenos">544</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
</span><span id="CodeTypeParser.__init__-545"><a href="#CodeTypeParser.__init__-545"><span class="linenos">545</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
</span><span id="CodeTypeParser.__init__-546"><a href="#CodeTypeParser.__init__-546"><span class="linenos">546</span></a> <span class="sa">f</span><span class="s2">"Cannot initialise parsers as the TRUD processed directory </span><span class="si">{</span><span class="n">trud_processed_dir</span><span class="si">}</span><span class="s2"> does not exist, please check that TRUD has been installed: acmc trud install"</span>
</span><span id="CodeTypeParser.__init__-547"><a href="#CodeTypeParser.__init__-547"><span class="linenos">547</span></a> <span class="p">)</span>
</span><span id="CodeTypeParser.__init__-548"><a href="#CodeTypeParser.__init__-548"><span class="linenos">548</span></a>
</span><span id="CodeTypeParser.__init__-549"><a href="#CodeTypeParser.__init__-549"><span class="linenos">549</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">code_types</span> <span class="o">=</span> <span class="p">{</span>
</span><span id="CodeTypeParser.__init__-550"><a href="#CodeTypeParser.__init__-550"><span class="linenos">550</span></a> <span class="s2">"read2"</span><span class="p">:</span> <span class="n">Read2</span><span class="p">(),</span>
</span><span id="CodeTypeParser.__init__-551"><a href="#CodeTypeParser.__init__-551"><span class="linenos">551</span></a> <span class="s2">"read3"</span><span class="p">:</span> <span class="n">Read3</span><span class="p">(),</span>
</span><span id="CodeTypeParser.__init__-552"><a href="#CodeTypeParser.__init__-552"><span class="linenos">552</span></a> <span class="s2">"icd10"</span><span class="p">:</span> <span class="n">Icd10</span><span class="p">(),</span>
</span><span id="CodeTypeParser.__init__-553"><a href="#CodeTypeParser.__init__-553"><span class="linenos">553</span></a> <span class="s2">"snomed"</span><span class="p">:</span> <span class="n">Snomed</span><span class="p">(),</span>
</span><span id="CodeTypeParser.__init__-554"><a href="#CodeTypeParser.__init__-554"><span class="linenos">554</span></a> <span class="s2">"opcs4"</span><span class="p">:</span> <span class="n">Opcs4</span><span class="p">(),</span>
</span><span id="CodeTypeParser.__init__-555"><a href="#CodeTypeParser.__init__-555"><span class="linenos">555</span></a> <span class="s2">"atc"</span><span class="p">:</span> <span class="n">Atc</span><span class="p">(),</span>
</span><span id="CodeTypeParser.__init__-556"><a href="#CodeTypeParser.__init__-556"><span class="linenos">556</span></a> <span class="s2">"med"</span><span class="p">:</span> <span class="n">Med</span><span class="p">(),</span>
</span><span id="CodeTypeParser.__init__-557"><a href="#CodeTypeParser.__init__-557"><span class="linenos">557</span></a> <span class="s2">"cprd"</span><span class="p">:</span> <span class="n">Cprd</span><span class="p">(),</span>
</span><span id="CodeTypeParser.__init__-558"><a href="#CodeTypeParser.__init__-558"><span class="linenos">558</span></a> <span class="p">}</span>
</span></pre></div>
</div>
<div id="CodeTypeParser.code_types" class="classattr">
<div class="attr variable">
<span class="name">code_types</span>
</div>
<a class="headerlink" href="#CodeTypeParser.code_types"></a>
</div>
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