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@kevinschaper
kevinschaper committed Oct 4, 2024
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35 changes: 35 additions & 0 deletions docs/Usage/CLI/index.html
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</label>
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>

<li class="md-nav__item">
<a href="#koza-split" class="md-nav__link">
<span class="md-ellipsis">
koza split
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#koza-transform" class="md-nav__link">
<span class="md-ellipsis">
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</label>
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>

<li class="md-nav__item">
<a href="#koza-split" class="md-nav__link">
<span class="md-ellipsis">
koza split
</span>
</a>

</li>

<li class="md-nav__item">
<a href="#koza-transform" class="md-nav__link">
<span class="md-ellipsis">
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</ul>
<p><strong>Commands</strong>:</p>
<ul>
<li><code>split</code>: Split a file by fields</li>
<li><code>transform</code>: Transform a source file</li>
<li><code>validate</code>: Validate a source file</li>
</ul>
<h2 id="koza-split"><code>koza split</code></h2>
<p>Split a file by fields</p>
<p><strong>Usage</strong>:</p>
<div class="highlight"><pre><span></span><code><span class="gp">$ </span>koza<span class="w"> </span>split<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span><span class="w"> </span>FILE<span class="w"> </span>FIELDS
</code></pre></div>
<p><strong>Arguments</strong>:</p>
<ul>
<li><code>FILE</code>: Path to the source kgx file to be split [required]</li>
<li><code>FIELDS</code>: Comma separated list of fields to split on [required]</li>
</ul>
<p><strong>Options</strong>:</p>
<ul>
<li><code>--remove-prefixes / --no-remove-prefixes</code>: Remove prefixes from the file names for values from the specified fields. (e.g, NCBIGene:9606 becomes 9606 [default: no-remove-prefixes]</li>
<li><code>--output-dir TEXT</code>: Path to output directory [default: output]</li>
<li><code>--help</code>: Show this message and exit.</li>
</ul>
<h2 id="koza-transform"><code>koza transform</code></h2>
<p>Transform a source file</p>
<p><strong>Usage</strong>:</p>
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Expand Up @@ -758,16 +758,16 @@ <h2 id="src.koza.cli_utils.get_koza_app" class="doc doc-heading">

<details class="quote">
<summary>Source code in <code>src/koza/cli_utils.py</code></summary>
<div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">26</span>
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<span class="normal">35</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_koza_app</span><span class="p">(</span><span class="n">source_name</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Optional</span><span class="p">[</span><span class="n">KozaApp</span><span class="p">]:</span>
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<span class="normal">36</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_koza_app</span><span class="p">(</span><span class="n">source_name</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Optional</span><span class="p">[</span><span class="n">KozaApp</span><span class="p">]:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Return a KozaApp object for a given source</span>

<span class="sd"> Args:</span>
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<details class="quote">
<summary>Source code in <code>src/koza/cli_utils.py</code></summary>
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<span class="n">global_table</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">local_table</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">logger</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
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<details class="quote">
<summary>Source code in <code>src/koza/cli_utils.py</code></summary>
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<span class="n">source</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">output_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="n">output_format</span><span class="p">:</span> <span class="n">OutputFormat</span> <span class="o">=</span> <span class="n">OutputFormat</span><span class="p">(</span><span class="s2">&quot;tsv&quot;</span><span class="p">),</span>
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<details class="quote">
<summary>Source code in <code>src/koza/cli_utils.py</code></summary>
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<span class="n">file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
<span class="nb">format</span><span class="p">:</span> <span class="n">FormatType</span> <span class="o">=</span> <span class="n">FormatType</span><span class="o">.</span><span class="n">csv</span><span class="p">,</span>
<span class="n">delimiter</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;,&quot;</span><span class="p">,</span>
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16 changes: 8 additions & 8 deletions docs/sitemap.xml
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<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
<url>
<loc>https://koza.monarchinitiative.org/</loc>
<lastmod>2024-08-20</lastmod>
<lastmod>2024-10-04</lastmod>
<changefreq>daily</changefreq>
</url>
<url>
<loc>https://koza.monarchinitiative.org/Ingests/</loc>
<lastmod>2024-08-20</lastmod>
<lastmod>2024-10-04</lastmod>
<changefreq>daily</changefreq>
</url>
<url>
<loc>https://koza.monarchinitiative.org/Ingests/mapping/</loc>
<lastmod>2024-08-20</lastmod>
<lastmod>2024-10-04</lastmod>
<changefreq>daily</changefreq>
</url>
<url>
<loc>https://koza.monarchinitiative.org/Ingests/source_config/</loc>
<lastmod>2024-08-20</lastmod>
<lastmod>2024-10-04</lastmod>
<changefreq>daily</changefreq>
</url>
<url>
<loc>https://koza.monarchinitiative.org/Ingests/testing/</loc>
<lastmod>2024-08-20</lastmod>
<lastmod>2024-10-04</lastmod>
<changefreq>daily</changefreq>
</url>
<url>
<loc>https://koza.monarchinitiative.org/Ingests/transform/</loc>
<lastmod>2024-08-20</lastmod>
<lastmod>2024-10-04</lastmod>
<changefreq>daily</changefreq>
</url>
<url>
<loc>https://koza.monarchinitiative.org/Usage/CLI/</loc>
<lastmod>2024-08-20</lastmod>
<lastmod>2024-10-04</lastmod>
<changefreq>daily</changefreq>
</url>
<url>
<loc>https://koza.monarchinitiative.org/Usage/Module/</loc>
<lastmod>2024-08-20</lastmod>
<lastmod>2024-10-04</lastmod>
<changefreq>daily</changefreq>
</url>
</urlset>
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