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feat(file_name): actually support updating filename if provided in in… (#51)
* feat(file_name): actually support updating filename if provided in indexing manifest * Apply automatic documentation changes Co-authored-by: Alexander VT <[email protected]>
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‎docs/_build/html/_modules/gen3/auth.html‎

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<title>gen3.auth &#8212; Gen3 SDK documentation</title>
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‎docs/_build/html/_modules/gen3/file.html‎

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<title>gen3.index &#8212; Gen3 SDK documentation</title>
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‎docs/_build/html/_modules/gen3/metadata.html‎

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‎docs/_build/html/_modules/gen3/submission.html‎

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‎docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html‎

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<title>gen3.tools.indexing.download_manifest &#8212; Gen3 SDK documentation</title>
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‎docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html‎

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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>gen3.tools.indexing.index_manifest &#8212; Gen3 SDK documentation</title>
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@@ -182,8 +183,8 @@ <h1>Source code for gen3.tools.indexing.index_manifest</h1><div class="highlight
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<span class="n">fieldnames</span><span class="p">[</span><span class="n">fieldnames</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">key</span><span class="p">)]</span> <span class="o">=</span> <span class="s2">&quot;guid&quot;</span>
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<span class="n">standardized_key</span> <span class="o">=</span> <span class="s2">&quot;guid&quot;</span>
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<span class="k">elif</span> <span class="n">key</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">FILENAME</span><span class="p">:</span>
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<span class="n">fieldnames</span><span class="p">[</span><span class="n">fieldnames</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">key</span><span class="p">)]</span> <span class="o">=</span> <span class="s2">&quot;filename&quot;</span>
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<span class="n">standardized_key</span> <span class="o">=</span> <span class="s2">&quot;filename&quot;</span>
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<span class="n">fieldnames</span><span class="p">[</span><span class="n">fieldnames</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">key</span><span class="p">)]</span> <span class="o">=</span> <span class="s2">&quot;file_name&quot;</span>
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<span class="n">standardized_key</span> <span class="o">=</span> <span class="s2">&quot;file_name&quot;</span>
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<span class="k">elif</span> <span class="n">key</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">MD5</span><span class="p">:</span>
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<span class="n">fieldnames</span><span class="p">[</span><span class="n">fieldnames</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">key</span><span class="p">)]</span> <span class="o">=</span> <span class="s2">&quot;md5&quot;</span>
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<span class="n">standardized_key</span> <span class="o">=</span> <span class="s2">&quot;md5&quot;</span>
@@ -340,6 +341,11 @@ <h1>Source code for gen3.tools.indexing.index_manifest</h1><div class="highlight
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<span class="k">else</span><span class="p">:</span>
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<span class="n">acl</span> <span class="o">=</span> <span class="p">[]</span>
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<span class="k">if</span> <span class="s2">&quot;file_name&quot;</span> <span class="ow">in</span> <span class="n">fi</span><span class="p">:</span>
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<span class="n">file_name</span> <span class="o">=</span> <span class="n">_standardize_str</span><span class="p">(</span><span class="n">fi</span><span class="p">[</span><span class="s2">&quot;file_name&quot;</span><span class="p">])</span>
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<span class="k">else</span><span class="p">:</span>
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<span class="n">file_name</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
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<span class="n">doc</span> <span class="o">=</span> <span class="kc">None</span>
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<span class="k">if</span> <span class="n">fi</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;guid&quot;</span><span class="p">):</span>
@@ -381,6 +387,10 @@ <h1>Source code for gen3.tools.indexing.index_manifest</h1><div class="highlight
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<span class="n">doc</span><span class="o">.</span><span class="n">authz</span> <span class="o">=</span> <span class="n">authz</span>
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<span class="n">need_update</span> <span class="o">=</span> <span class="kc">True</span>
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<span class="k">if</span> <span class="n">doc</span><span class="o">.</span><span class="n">file_name</span> <span class="o">!=</span> <span class="n">file_name</span><span class="p">:</span>
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<span class="n">doc</span><span class="o">.</span><span class="n">file_name</span> <span class="o">=</span> <span class="n">file_name</span>
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<span class="n">need_update</span> <span class="o">=</span> <span class="kc">True</span>
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<span class="k">if</span> <span class="n">need_update</span><span class="p">:</span>
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<span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;updating </span><span class="si">{</span><span class="n">doc</span><span class="o">.</span><span class="n">did</span><span class="si">}</span><span class="s2"> to: </span><span class="si">{</span><span class="n">doc</span><span class="o">.</span><span class="n">to_json</span><span class="p">()</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
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<span class="n">doc</span><span class="o">.</span><span class="n">patch</span><span class="p">()</span>
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<span class="s2">&quot;acl&quot;</span><span class="p">:</span> <span class="n">acl</span><span class="p">,</span>
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<span class="s2">&quot;authz&quot;</span><span class="p">:</span> <span class="n">authz</span><span class="p">,</span>
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<span class="s2">&quot;urls&quot;</span><span class="p">:</span> <span class="n">urls</span><span class="p">,</span>
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<span class="s2">&quot;file_name&quot;</span><span class="p">:</span> <span class="n">file_name</span><span class="p">,</span>
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<span class="p">}</span>
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<span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;creating: </span><span class="si">{</span><span class="n">record</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
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<span class="n">doc</span> <span class="o">=</span> <span class="n">indexclient</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="o">**</span><span class="n">record</span><span class="p">)</span>

‎docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html‎

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‎docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html‎

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‎docs/_build/html/_modules/index.html‎

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