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<li class="toctree-l1"><a class="reference internal" href="../../modules/src.html">HDF5 data operations</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../modules/src.html#module-src.hdf5_lib">Data integration with HDF5</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../modules/src.html#module-src.metadata_review_lib">Data annotation and review</a></li>
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<h1>Source code for src.data_integration_lib</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">src.hdf5_lib</span> <span class="k">as</span> <span class="nn">hdf5_lib</span>
<span class="kn">import</span> <span class="nn">src.g5505_utils</span> <span class="k">as</span> <span class="nn">utils</span>
<span class="kn">import</span> <span class="nn">yaml</span>
<span class="kn">import</span> <span class="nn">logging</span>
<span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">datetime</span>
<div class="viewcode-block" id="integrate_data_sources">
<a class="viewcode-back" href="../../modules/src.html#src.data_integration_lib.integrate_data_sources">[docs]</a>
<span class="k">def</span> <span class="nf">integrate_data_sources</span><span class="p">(</span><span class="n">yaml_config_file_path</span><span class="p">,</span> <span class="n">log_dir</span><span class="o">=</span><span class="s1">&#39;logs/&#39;</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot; Integrates data sources specified by the input configuration file into HDF5 files.</span>
<span class="sd"> Parameters:</span>
<span class="sd"> yaml_config_file_path (str): Path to the YAML configuration file.</span>
<span class="sd"> log_dir (str): Directory to save the log file.</span>
<span class="sd"> Returns:</span>
<span class="sd"> str: Path (or list of Paths) to the created HDF5 file(s).</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">date</span> <span class="o">=</span> <span class="n">utils</span><span class="o">.</span><span class="n">created_at</span><span class="p">()</span>
<span class="n">utils</span><span class="o">.</span><span class="n">setup_logging</span><span class="p">(</span><span class="n">log_dir</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;integrate_data_sources_</span><span class="si">{</span><span class="n">date</span><span class="si">}</span><span class="s2">.log&quot;</span><span class="p">)</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">yaml_config_file_path</span><span class="p">,</span><span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">stream</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">config_dict</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">stream</span><span class="p">,</span> <span class="n">Loader</span><span class="o">=</span><span class="n">yaml</span><span class="o">.</span><span class="n">FullLoader</span><span class="p">)</span>
<span class="k">except</span> <span class="n">yaml</span><span class="o">.</span><span class="n">YAMLError</span> <span class="k">as</span> <span class="n">exc</span><span class="p">:</span>
<span class="n">logging</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">&quot;Error loading YAML file: </span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">exc</span><span class="p">)</span>
<span class="k">raise</span>
<span class="k">def</span> <span class="nf">output_filename</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">date</span><span class="p">,</span> <span class="n">initials</span><span class="p">):</span>
<span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">date</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">initials</span><span class="si">}</span><span class="s2">.h5&quot;</span>
<span class="n">exp_campaign_name</span> <span class="o">=</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;experiment&#39;</span><span class="p">]</span>
<span class="n">initials</span> <span class="o">=</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;contact&#39;</span><span class="p">]</span>
<span class="n">input_file_dir</span> <span class="o">=</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;input_file_directory&#39;</span><span class="p">]</span>
<span class="n">output_dir</span> <span class="o">=</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;output_file_directory&#39;</span><span class="p">]</span>
<span class="n">select_dir_keywords</span> <span class="o">=</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;instrument_datafolder&#39;</span><span class="p">]</span>
<span class="n">root_metadata_dict</span> <span class="o">=</span> <span class="p">{</span>
<span class="s1">&#39;project&#39;</span> <span class="p">:</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;project&#39;</span><span class="p">],</span>
<span class="s1">&#39;experiment&#39;</span> <span class="p">:</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;experiment&#39;</span><span class="p">],</span>
<span class="s1">&#39;contact&#39;</span> <span class="p">:</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;contact&#39;</span><span class="p">],</span>
<span class="s1">&#39;actris_level&#39;</span><span class="p">:</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;actris_level&#39;</span><span class="p">]</span>
<span class="p">}</span>
<span class="k">def</span> <span class="nf">create_hdf5_file</span><span class="p">(</span><span class="n">date_str</span><span class="p">,</span> <span class="n">select_file_keywords</span><span class="p">,</span><span class="n">root_metadata</span><span class="p">):</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">output_filename</span><span class="p">(</span><span class="n">exp_campaign_name</span><span class="p">,</span> <span class="n">date_str</span><span class="p">,</span> <span class="n">initials</span><span class="p">)</span>
<span class="n">output_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
<span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Creating HDF5 file at: </span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">output_path</span><span class="p">)</span>
<span class="k">return</span> <span class="n">hdf5_lib</span><span class="o">.</span><span class="n">create_hdf5_file_from_filesystem_path</span><span class="p">(</span>
<span class="n">output_path</span><span class="p">,</span> <span class="n">input_file_dir</span><span class="p">,</span> <span class="n">select_dir_keywords</span><span class="p">,</span> <span class="n">select_file_keywords</span><span class="p">,</span> <span class="n">root_metadata_dict</span><span class="o">=</span><span class="n">root_metadata</span>
<span class="p">)</span>
<span class="k">if</span> <span class="n">config_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;datetime_steps&#39;</span><span class="p">):</span>
<span class="n">datetime_augment_dict</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">datetime_step</span> <span class="ow">in</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;datetime_steps&#39;</span><span class="p">]:</span>
<span class="n">tmp</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">strptime</span><span class="p">(</span><span class="n">datetime_step</span><span class="p">,</span><span class="s1">&#39;%Y-%m-</span><span class="si">%d</span><span class="s1"> %H-%M-%S&#39;</span><span class="p">)</span> <span class="c1">#convert(datetime_step)</span>
<span class="n">datetime_augment_dict</span><span class="p">[</span><span class="n">tmp</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">tmp</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">&#39;%Y-%m-</span><span class="si">%d</span><span class="s1">&#39;</span><span class="p">),</span><span class="n">tmp</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">&#39;%Y_%m_</span><span class="si">%d</span><span class="s1">&#39;</span><span class="p">),</span><span class="n">tmp</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">&#39;%Y.%m.</span><span class="si">%d</span><span class="s1">&#39;</span><span class="p">),</span><span class="n">tmp</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">&#39;%Y%m</span><span class="si">%d</span><span class="s1">&#39;</span><span class="p">)]</span>
<span class="nb">print</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span>
<span class="k">if</span> <span class="s1">&#39;single_experiment&#39;</span> <span class="ow">in</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;integration_mode&#39;</span><span class="p">]:</span>
<span class="n">output_filename_path</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">datetime_step</span> <span class="ow">in</span> <span class="n">datetime_augment_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">date_str</span> <span class="o">=</span> <span class="n">datetime_step</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">&#39;%Y-%m-</span><span class="si">%d</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">select_file_keywords</span> <span class="o">=</span> <span class="n">datetime_augment_dict</span><span class="p">[</span><span class="n">datetime_step</span><span class="p">]</span>
<span class="n">root_metadata_dict</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;dataset_startdate&#39;</span><span class="p">:</span> <span class="n">date_str</span><span class="p">,</span>
<span class="s1">&#39;dataset_enddate&#39;</span><span class="p">:</span> <span class="n">date_str</span><span class="p">})</span>
<span class="n">dt_step_output_filename_path</span><span class="o">=</span> <span class="n">create_hdf5_file</span><span class="p">(</span><span class="n">date_str</span><span class="p">,</span> <span class="n">select_file_keywords</span><span class="p">,</span> <span class="n">root_metadata_dict</span><span class="p">)</span>
<span class="n">output_filename_path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dt_step_output_filename_path</span><span class="p">)</span>
<span class="k">elif</span> <span class="s1">&#39;collection&#39;</span> <span class="ow">in</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;integration_mode&#39;</span><span class="p">]:</span>
<span class="n">select_file_keywords</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">datetime_step</span> <span class="ow">in</span> <span class="n">datetime_augment_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">select_file_keywords</span> <span class="o">=</span> <span class="n">select_file_keywords</span> <span class="o">+</span> <span class="n">datetime_augment_dict</span><span class="p">[</span><span class="n">datetime_step</span><span class="p">]</span>
<span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;dataset_startdate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">datetime_augment_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
<span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;dataset_enddate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">datetime_augment_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
<span class="n">startdate</span> <span class="o">=</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;dataset_startdate&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">&#39;%Y-%m-</span><span class="si">%d</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">enddate</span> <span class="o">=</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;dataset_enddate&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s1">&#39;%Y-%m-</span><span class="si">%d</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">root_metadata_dict</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;dataset_startdate&#39;</span><span class="p">:</span> <span class="n">startdate</span><span class="p">,</span>
<span class="s1">&#39;dataset_enddate&#39;</span><span class="p">:</span> <span class="n">enddate</span><span class="p">})</span>
<span class="n">date_str</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">startdate</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">enddate</span><span class="si">}</span><span class="s1">&#39;</span>
<span class="n">output_filename_path</span> <span class="o">=</span> <span class="n">create_hdf5_file</span><span class="p">(</span><span class="n">date_str</span><span class="p">,</span> <span class="n">select_file_keywords</span><span class="p">,</span> <span class="n">root_metadata_dict</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">startdate</span> <span class="o">=</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;dataset_startdate&#39;</span><span class="p">]</span>
<span class="n">enddate</span> <span class="o">=</span> <span class="n">config_dict</span><span class="p">[</span><span class="s1">&#39;dataset_enddate&#39;</span><span class="p">]</span>
<span class="n">root_metadata_dict</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;dataset_startdate&#39;</span><span class="p">:</span> <span class="n">startdate</span><span class="p">,</span>
<span class="s1">&#39;dataset_enddate&#39;</span><span class="p">:</span> <span class="n">enddate</span><span class="p">})</span>
<span class="n">date_str</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">startdate</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">enddate</span><span class="si">}</span><span class="s1">&#39;</span>
<span class="n">output_filename_path</span> <span class="o">=</span> <span class="n">create_hdf5_file</span><span class="p">(</span><span class="n">date_str</span><span class="p">,</span> <span class="n">select_file_keywords</span> <span class="o">=</span> <span class="p">[],</span> <span class="n">root_metadata</span> <span class="o">=</span> <span class="n">root_metadata_dict</span><span class="p">)</span>
<span class="k">return</span> <span class="n">output_filename_path</span></div>
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