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feat(objects): expand download options to include the python command … #176

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Feb 20, 2023
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feat(objects): expand download options to include the python command … #176

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feat(objects): expand download options to include the python command …
Avantol13 Feb 20, 2023
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Avantol13 Feb 20, 2023
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Avantol13 Feb 20, 2023
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Avantol13 Feb 20, 2023
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15 changes: 13 additions & 2 deletions docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html
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Expand Up @@ -96,6 +96,7 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli
<span class="n">num_processes</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
<span class="n">max_concurrent_requests</span><span class="o">=</span><span class="n">MAX_CONCURRENT_REQUESTS</span><span class="p">,</span>
<span class="n">input_manifest</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">python_subprocess_command</span><span class="o">=</span><span class="s2">&quot;python&quot;</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Download all file object records into a manifest csv</span>
Expand All @@ -111,6 +112,10 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli
<span class="sd"> input_manifest (str): Input file. Read available object data from objects in this</span>
<span class="sd"> file instead of reading everything in indexd. This will attempt to query</span>
<span class="sd"> indexd for only the records identified in this manifest.</span>
<span class="sd"> python_subprocess_command (str, optional): Command used to execute a</span>
<span class="sd"> python process. By default you should not need to change this, but</span>
<span class="sd"> if you are running something like MacOS and only installed Python 3.x</span>
<span class="sd"> you may need to specify &quot;python3&quot;.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">start_time</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">perf_counter</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="sa">f</span><span class="s2">&quot;start time: </span><span class="si">{</span><span class="n">start_time</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
Expand Down Expand Up @@ -140,6 +145,7 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli
<span class="n">num_processes</span><span class="p">,</span>
<span class="n">max_concurrent_requests</span><span class="p">,</span>
<span class="n">input_manifest</span><span class="p">,</span>
<span class="n">python_subprocess_command</span><span class="p">,</span>
<span class="p">)</span>

<span class="n">end_time</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">perf_counter</span><span class="p">()</span>
Expand All @@ -148,7 +154,12 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli


<span class="k">async</span> <span class="k">def</span> <span class="nf">_write_all_index_records_to_file</span><span class="p">(</span>
<span class="n">commons_url</span><span class="p">,</span> <span class="n">output_filename</span><span class="p">,</span> <span class="n">num_processes</span><span class="p">,</span> <span class="n">max_concurrent_requests</span><span class="p">,</span> <span class="n">input_manifest</span>
<span class="n">commons_url</span><span class="p">,</span>
<span class="n">output_filename</span><span class="p">,</span>
<span class="n">num_processes</span><span class="p">,</span>
<span class="n">max_concurrent_requests</span><span class="p">,</span>
<span class="n">input_manifest</span><span class="p">,</span>
<span class="n">python_subprocess_command</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Spins up number of processes provided to parse indexd records and eventually</span>
Expand Down Expand Up @@ -233,7 +244,7 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli

<span class="c1"># call the cli function below and pass in chunks of pages for each process</span>
<span class="n">command</span> <span class="o">=</span> <span class="p">(</span>
<span class="sa">f</span><span class="s2">&quot;python </span><span class="si">{</span><span class="n">CURRENT_DIR</span><span class="si">}</span><span class="s2">/download_manifest.py --commons_url &quot;</span>
<span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">python_subprocess_command</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">CURRENT_DIR</span><span class="si">}</span><span class="s2">/download_manifest.py --commons_url &quot;</span>
<span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">commons_url</span><span class="si">}</span><span class="s2"> --pages </span><span class="si">{</span><span class="n">pages</span><span class="si">}</span><span class="s2"> --input-record-chunks-file </span><span class="si">{</span><span class="n">input_records_chunk_filename</span><span class="si">}</span><span class="s2"> &quot;</span>
<span class="sa">f</span><span class="s2">&quot;--num_processes </span><span class="si">{</span><span class="n">num_processes</span><span class="si">}</span><span class="s2"> --max_concurrent_requests </span><span class="si">{</span><span class="n">max_concurrent_requests</span><span class="si">}</span><span class="s2">&quot;</span>
<span class="p">)</span>
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2 changes: 1 addition & 1 deletion docs/_build/html/searchindex.js
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8 changes: 6 additions & 2 deletions docs/_build/html/tools/indexing.html
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Expand Up @@ -96,7 +96,7 @@ <h1>Indexing Tools<a class="headerlink" href="#indexing-tools" title="Permalink

<dl class="py function">
<dt class="sig sig-object py" id="gen3.tools.indexing.download_manifest.async_download_object_manifest">
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.download_manifest.</span></span><span class="sig-name descname"><span class="pre">async_download_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'object-manifest.csv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_processes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_manifest</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/download_manifest.html#async_download_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.download_manifest.async_download_object_manifest" title="Permalink to this definition">¶</a></dt>
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.download_manifest.</span></span><span class="sig-name descname"><span class="pre">async_download_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'object-manifest.csv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_processes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_manifest</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">python_subprocess_command</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'python'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/download_manifest.html#async_download_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.download_manifest.async_download_object_manifest" title="Permalink to this definition">¶</a></dt>
<dd><p>Download all file object records into a manifest csv</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
Expand All @@ -111,6 +111,10 @@ <h1>Indexing Tools<a class="headerlink" href="#indexing-tools" title="Permalink
<li><p><strong>input_manifest</strong> (<em>str</em>) – Input file. Read available object data from objects in this
file instead of reading everything in indexd. This will attempt to query
indexd for only the records identified in this manifest.</p></li>
<li><p><strong>python_subprocess_command</strong> (<em>str</em><em>, </em><em>optional</em>) – Command used to execute a
python process. By default you should not need to change this, but
if you are running something like MacOS and only installed Python 3.x
you may need to specify “python3”.</p></li>
</ul>
</dd>
</dl>
Expand Down Expand Up @@ -377,7 +381,7 @@ <h1>Indexing Tools<a class="headerlink" href="#indexing-tools" title="Permalink

<dl class="py function">
<dt class="sig sig-object py" id="gen3.tools.indexing.verify_manifest.async_verify_object_manifest">
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1674497076.8602023.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Permalink to this definition">¶</a></dt>
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1676929361.016488.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Permalink to this definition">¶</a></dt>
<dd><p>Verify all file object records into a manifest csv</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
Expand Down
2 changes: 1 addition & 1 deletion docs/_build/html/tools/metadata.html
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Expand Up @@ -102,7 +102,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Permalink

<dl class="py function">
<dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest">
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1674497077.2165172.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Permalink to this definition">¶</a></dt>
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1676929361.398911.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Permalink to this definition">¶</a></dt>
<dd><p>Ingest all metadata records into a manifest csv</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
Expand Down
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