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brain-bican · Nov 7, 2024 · a0ec057 · a0ec057
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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: acfbbaecd20da8e792384ef7f306c5ac
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/bkbit.cli.doctree b/.doctrees/bkbit.cli.doctree
diff --git a/.doctrees/bkbit.data_translators.anatomical_structure_translator.doctree b/.doctrees/bkbit.data_translators.anatomical_structure_translator.doctree
diff --git a/.doctrees/bkbit.data_translators.doctree b/.doctrees/bkbit.data_translators.doctree
diff --git a/.doctrees/bkbit.data_translators.file_manifest_translator.doctree b/.doctrees/bkbit.data_translators.file_manifest_translator.doctree
diff --git a/.doctrees/bkbit.data_translators.genome_annotation_translator.doctree b/.doctrees/bkbit.data_translators.genome_annotation_translator.doctree
diff --git a/.doctrees/bkbit.data_translators.library_generation_translator.doctree b/.doctrees/bkbit.data_translators.library_generation_translator.doctree
diff --git a/.doctrees/bkbit.data_translators.specimen_metadata_translator.doctree b/.doctrees/bkbit.data_translators.specimen_metadata_translator.doctree
diff --git a/.doctrees/bkbit.doctree b/.doctrees/bkbit.doctree
diff --git a/.doctrees/bkbit.model_converters.doctree b/.doctrees/bkbit.model_converters.doctree
diff --git a/.doctrees/bkbit.model_converters.sheets_converter.doctree b/.doctrees/bkbit.model_converters.sheets_converter.doctree
diff --git a/.doctrees/bkbit.model_converters.yaml2sheet_converter.doctree b/.doctrees/bkbit.model_converters.yaml2sheet_converter.doctree
diff --git a/.doctrees/bkbit.model_editors.add_dunderMethods_genomeAnnotation.doctree b/.doctrees/bkbit.model_editors.add_dunderMethods_genomeAnnotation.doctree
diff --git a/.doctrees/bkbit.model_editors.doctree b/.doctrees/bkbit.model_editors.doctree
diff --git a/.doctrees/bkbit.model_editors.linkml_trimmer.doctree b/.doctrees/bkbit.model_editors.linkml_trimmer.doctree
diff --git a/.doctrees/bkbit.models.anatomical_structure.doctree b/.doctrees/bkbit.models.anatomical_structure.doctree
diff --git a/.doctrees/bkbit.models.doctree b/.doctrees/bkbit.models.doctree
diff --git a/.doctrees/bkbit.models.genome_annotation.doctree b/.doctrees/bkbit.models.genome_annotation.doctree
diff --git a/.doctrees/bkbit.models.library_generation.doctree b/.doctrees/bkbit.models.library_generation.doctree
diff --git a/.doctrees/bkbit.utils.doctree b/.doctrees/bkbit.utils.doctree
diff --git a/.doctrees/bkbit.utils.get_ncbi_taxonomy.doctree b/.doctrees/bkbit.utils.get_ncbi_taxonomy.doctree
diff --git a/.doctrees/bkbit.utils.load_json.doctree b/.doctrees/bkbit.utils.load_json.doctree
diff --git a/.doctrees/bkbit.utils.nimp_api_endpoints.doctree b/.doctrees/bkbit.utils.nimp_api_endpoints.doctree
diff --git a/.doctrees/bkbit.utils.setup_logger.doctree b/.doctrees/bkbit.utils.setup_logger.doctree
diff --git a/.doctrees/contributing.doctree b/.doctrees/contributing.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/genome_annotation.doctree b/.doctrees/genome_annotation.doctree
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/install.doctree b/.doctrees/install.doctree
diff --git a/.doctrees/linkml_trimmer.doctree b/.doctrees/linkml_trimmer.doctree
diff --git a/.doctrees/modules.doctree b/.doctrees/modules.doctree
diff --git a/.doctrees/quickstart.doctree b/.doctrees/quickstart.doctree
diff --git a/.doctrees/specimen_file_manifest.doctree b/.doctrees/specimen_file_manifest.doctree
diff --git a/.doctrees/specimen_metadata.doctree b/.doctrees/specimen_metadata.doctree
diff --git a/.doctrees/spreadsheet_converter.doctree b/.doctrees/spreadsheet_converter.doctree
diff --git a/.nojekyll b/.nojekyll
diff --git a/_modules/bkbit/data_translators/anatomical_structure_translator.html b/_modules/bkbit/data_translators/anatomical_structure_translator.html
diff --git a/_modules/bkbit/data_translators/genome_annotation_translator.html b/_modules/bkbit/data_translators/genome_annotation_translator.html
diff --git a/_modules/bkbit/data_translators/specimen_metadata_translator.html b/_modules/bkbit/data_translators/specimen_metadata_translator.html
@@ -0,0 +1,159 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../../../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>bkbit.data_translators.specimen_metadata_translator &mdash; bkbit  documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=80d5e7a1" />
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+    <input type="hidden" name="area" value="default" />
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+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">GETTING STARTED</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">DATA TRANSLATORS</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../../specimen_file_manifest.html">Specimen File Manifest</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../specimen_metadata.html">Specimen Metadata</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../genome_annotation.html">Annotated Genome Data</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">MODEL CONVERTERS</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../../spreadsheet_converter.html">Spreadsheet to LinkML Schema</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">MODEL EDITORS</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../../linkml_trimmer.html">LinkML Schema Trimmer</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">REFERENCE</span></p>
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+          <li class="breadcrumb-item"><a href="../../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">bkbit.data_translators.specimen_metadata_translator</li>
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+
+  <h1>Source code for bkbit.data_translators.specimen_metadata_translator</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">click</span>
+
+<div class="viewcode-block" id="extract_specimen_ids">
+<a class="viewcode-back" href="../../../bkbit.data_translators.specimen_metadata_translator.html#bkbit.data_translators.specimen_metadata_translator.extract_specimen_ids">[docs]</a>
+<span class="k">def</span> <span class="nf">extract_specimen_ids</span><span class="p">(</span><span class="n">csv_file_path</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Reads a CSV file and prints the &#39;Specimen ID&#39; column to the command line.</span>
+
+<span class="sd">    Parameters:</span>
+<span class="sd">    - csv_file_path: str, path to the input CSV file.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">csv_file_path</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">,</span> <span class="n">encoding</span><span class="o">=</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">csv_file</span><span class="p">:</span>
+        <span class="n">reader</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">csv_file</span><span class="p">)</span>
+
+        <span class="c1"># Ensure &#39;Specimen ID&#39; column exists in the CSV</span>
+        <span class="k">if</span> <span class="s1">&#39;Specimen ID&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">reader</span><span class="o">.</span><span class="n">fieldnames</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;The CSV file does not contain the &#39;Specimen ID&#39; column.&quot;</span><span class="p">)</span>
+
+        <span class="c1"># Print &#39;Specimen ID&#39; values to the command line</span>
+        <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">reader</span><span class="p">:</span>
+            <span class="n">specimen_id</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s1">&#39;Specimen ID&#39;</span><span class="p">]</span>
+            <span class="k">if</span> <span class="n">specimen_id</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;LA&quot;</span><span class="p">):</span>
+                <span class="nb">print</span><span class="p">(</span><span class="n">specimen_id</span><span class="p">)</span></div>
+
+
+<span class="nd">@click</span><span class="o">.</span><span class="n">command</span>
+<span class="nd">@click</span><span class="o">.</span><span class="n">argument</span><span class="p">(</span><span class="s1">&#39;specimen_metadata_file_path&#39;</span><span class="p">)</span>
+
+<span class="k">def</span> <span class="nf">list_library_aliquot</span><span class="p">(</span><span class="n">specimen_metadata_file_path</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Extracts and prints all the Library Aliquot NHash IDs from Data Catalog&#39;s specimen metadata file.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        specimen_metadata_file_path (str): Path to the specimen metadata file.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">extract_specimen_ids</span><span class="p">(</span><span class="n">specimen_metadata_file_path</span><span class="p">)</span>
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>  
+    <span class="n">list_library_aliquot</span><span class="p">()</span>
+</pre></div>
+
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