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<h1>Source code for bdc.pipeline</h1><div class="highlight"><pre>
<span></span><span class="c1"># SPDX-License-Identifier: MIT</span>
<span class="c1"># SPDX-FileCopyrightText: 2023 Lucca Baumgärtner &lt;lucca.baumgaertner@fau.de&gt;</span>
<span class="c1"># SPDX-FileCopyrightText: 2023 Sophie Heasman &lt;sophieheasmann@gmail.com&gt;</span>
<span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">datetime</span>

<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>

<span class="kn">from</span> <span class="nn">bdc.steps.step</span> <span class="kn">import</span> <span class="n">Step</span><span class="p">,</span> <span class="n">StepError</span>
<span class="kn">from</span> <span class="nn">database</span> <span class="kn">import</span> <span class="n">get_database</span>
<span class="kn">from</span> <span class="nn">logger</span> <span class="kn">import</span> <span class="n">get_logger</span>

<span class="n">log</span> <span class="o">=</span> <span class="n">get_logger</span><span class="p">()</span>


<div class="viewcode-block" id="Pipeline">
<a class="viewcode-back" href="../../bdc.html#bdc.pipeline.Pipeline">[docs]</a>
<span class="k">class</span> <span class="nc">Pipeline</span><span class="p">:</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">steps</span><span class="p">,</span>
<span class="n">limit</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">steps</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">Step</span><span class="p">]</span> <span class="o">=</span> <span class="n">steps</span>
<span class="bp">self</span><span class="o">.</span><span class="n">limit</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="n">limit</span>
<span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">get_database</span><span class="p">()</span><span class="o">.</span><span class="n">get_dataframe</span><span class="p">()</span>

<span class="k">if</span> <span class="n">limit</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[:</span><span class="n">limit</span><span class="p">]</span>

<div class="viewcode-block" id="Pipeline.run">
<a class="viewcode-back" href="../../bdc.html#bdc.pipeline.Pipeline.run">[docs]</a>
<span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">run_id</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s2">&quot;%Y/%m/</span><span class="si">%d</span><span class="s2">/%H%M%S/&quot;</span><span class="p">)</span>
<span class="n">error_occurred</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">log</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
<span class="s2">&quot;Error: DataFrame of pipeline has not been initialized, aborting pipeline run!&quot;</span>
<span class="p">)</span>
<span class="k">return</span>

<span class="c1"># helper to pass the dataframe and/or input location from previous step to next step</span>
<span class="k">for</span> <span class="n">step</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">steps</span><span class="p">:</span>
<span class="n">log</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Processing step </span><span class="si">{</span><span class="n">step</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="c1"># load dataframe and/or input location for this step</span>
<span class="k">if</span> <span class="n">step</span><span class="o">.</span><span class="n">df</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">step</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>

<span class="k">try</span><span class="p">:</span>
<span class="n">step</span><span class="o">.</span><span class="n">load_data</span><span class="p">()</span>
<span class="n">verified</span> <span class="o">=</span> <span class="n">step</span><span class="o">.</span><span class="n">verify</span><span class="p">()</span>
<span class="n">log</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Verification for step </span><span class="si">{</span><span class="n">step</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">verified</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="n">data_present</span> <span class="o">=</span> <span class="n">step</span><span class="o">.</span><span class="n">check_data_presence</span><span class="p">()</span>
<span class="k">if</span> <span class="n">verified</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">data_present</span><span class="p">:</span>
<span class="n">step_df</span> <span class="o">=</span> <span class="n">step</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">step_df</span>

<span class="c1"># cleanup</span>
<span class="n">step</span><span class="o">.</span><span class="n">finish</span><span class="p">()</span>
<span class="k">except</span> <span class="p">(</span><span class="n">StepError</span><span class="p">,</span> <span class="ne">Exception</span><span class="p">)</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
<span class="n">error_occurred</span> <span class="o">=</span> <span class="kc">True</span>
<span class="n">log</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Step </span><span class="si">{</span><span class="n">step</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2"> failed! </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">finally</span><span class="p">:</span>
<span class="c1"># Create snapshots to avoid data loss</span>
<span class="n">get_database</span><span class="p">()</span><span class="o">.</span><span class="n">create_snapshot</span><span class="p">(</span><span class="n">step</span><span class="o">.</span><span class="n">df</span><span class="p">,</span> <span class="n">prefix</span><span class="o">=</span><span class="n">run_id</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">step</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>

<span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>

<span class="c1"># Set dataframe in DAL</span>
<span class="n">get_database</span><span class="p">()</span><span class="o">.</span><span class="n">set_dataframe</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>

<span class="c1"># Upload DAL dataframe to chosen database</span>
<span class="n">get_database</span><span class="p">()</span><span class="o">.</span><span class="n">save_dataframe</span><span class="p">()</span>

<span class="c1"># Delete snapshots</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">error_occurred</span><span class="p">:</span>
<span class="n">get_database</span><span class="p">()</span><span class="o">.</span><span class="n">clean_snapshots</span><span class="p">(</span><span class="n">run_id</span><span class="p">)</span>

<span class="n">log</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Pipeline finished running </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">steps</span><span class="p">)</span><span class="si">}</span><span class="s2"> steps!&quot;</span><span class="p">)</span></div>
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