Chore/merge gsoc

.secrets.baseline

@@ -511,7 +511,7 @@
         "filename": "tests/test_file.py",
         "hashed_secret": "bc5494e9e5c7bd002f295376f6130e2eced73a4a",
         "is_verified": false,
-        "line_number": 84
+        "line_number": 86
       }
     ],
     "tests/test_index.py": [
@@ -656,5 +656,5 @@
       }
     ]
   },
-  "generated_at": "2025-11-07T21:07:45Z"
+  "generated_at": "2026-01-14T17:34:14Z"
 }

docs/_build/html/file.html

@@ -54,6 +54,12 @@ <h1>Gen3 File Class<a class="headerlink" href="#gen3-file-class" title="Link to
 <span class="gp">... </span><span class="n">file</span> <span class="o">=</span> <span class="n">Gen3File</span><span class="p">(</span><span class="n">auth</span><span class="p">)</span>
 </pre></div>
 </div>
+<dl class="py method">
+<dt class="sig sig-object py" id="gen3.file.Gen3File.async_download_multiple">
+<span class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></span><span class="sig-name descname"><span class="pre">async_download_multiple</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">manifest_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">download_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'original'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">protocol</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">max_concurrent_requests</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</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">3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">queue_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_completed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_progress</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gen3/file.html#Gen3File.async_download_multiple"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.file.Gen3File.async_download_multiple" title="Link to this definition">¶</a></dt>
+<dd><p>Asynchronously download multiple files using multiprocessing and queues.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gen3.file.Gen3File.delete_file">
 <span class="sig-name descname"><span class="pre">delete_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">guid</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gen3/file.html#Gen3File.delete_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.file.Gen3File.delete_file" title="Link to this definition">¶</a></dt>
@@ -91,7 +97,7 @@ <h1>Gen3 File Class<a class="headerlink" href="#gen3-file-class" title="Link to
 
 <dl class="py method">
 <dt class="sig sig-object py" id="gen3.file.Gen3File.download_single">
-<span class="sig-name descname"><span class="pre">download_single</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">object_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/gen3/file.html#Gen3File.download_single"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.file.Gen3File.download_single" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">download_single</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">object_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">protocol</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/file.html#Gen3File.download_single"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.file.Gen3File.download_single" title="Link to this definition">¶</a></dt>
 <dd><p>Download a single file using its GUID.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -100,6 +106,12 @@ <h1>Gen3 File Class<a class="headerlink" href="#gen3-file-class" title="Link to
 <li><p><strong>path</strong> (<em>str</em>) – Path to store the downloaded file at</p></li>
 </ul>
 </dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if download successful, False otherwise</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>bool</p>
+</dd>
 </dl>
 </dd></dl>
 
@@ -122,6 +134,26 @@ <h1>Gen3 File Class<a class="headerlink" href="#gen3-file-class" title="Link to
 </div>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="gen3.file.Gen3File.get_presigned_urls_batch">
+<span class="sig-name descname"><span class="pre">get_presigned_urls_batch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">guids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">protocol</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/file.html#Gen3File.get_presigned_urls_batch"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.file.Gen3File.get_presigned_urls_batch" title="Link to this definition">¶</a></dt>
+<dd><p>Get presigned URLs for multiple files efficiently.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>guids</strong> (<em>List</em><em>[</em><em>str</em><em>]</em>) – List of GUIDs to get presigned URLs for</p></li>
+<li><p><strong>protocol</strong> (<em>str</em><em>, </em><em>optional</em>) – Protocol preference for URLs</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Mapping of GUID to presigned URL response</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Dict[str, Dict]</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gen3.file.Gen3File.upload_file">
 <span class="sig-name descname"><span class="pre">upload_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">authz</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">protocol</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">expires_in</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">bucket</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/file.html#Gen3File.upload_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.file.Gen3File.upload_file" title="Link to this definition">¶</a></dt>
@@ -218,10 +250,12 @@ <h1 class="logo"><a href="index.html">Gen3 SDK</a></h1>
 <li class="toctree-l1"><a class="reference internal" href="auth.html">Gen3 Auth Helper</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Gen3 File Class</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#gen3.file.Gen3File"><code class="docutils literal notranslate"><span class="pre">Gen3File</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#gen3.file.Gen3File.async_download_multiple"><code class="docutils literal notranslate"><span class="pre">Gen3File.async_download_multiple()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.file.Gen3File.delete_file"><code class="docutils literal notranslate"><span class="pre">Gen3File.delete_file()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.file.Gen3File.delete_file_locations"><code class="docutils literal notranslate"><span class="pre">Gen3File.delete_file_locations()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.file.Gen3File.download_single"><code class="docutils literal notranslate"><span class="pre">Gen3File.download_single()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.file.Gen3File.get_presigned_url"><code class="docutils literal notranslate"><span class="pre">Gen3File.get_presigned_url()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#gen3.file.Gen3File.get_presigned_urls_batch"><code class="docutils literal notranslate"><span class="pre">Gen3File.get_presigned_urls_batch()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.file.Gen3File.upload_file"><code class="docutils literal notranslate"><span class="pre">Gen3File.upload_file()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.file.Gen3File.upload_file_to_guid"><code class="docutils literal notranslate"><span class="pre">Gen3File.upload_file_to_guid()</span></code></a></li>
 </ul>

docs/_build/html/genindex.html

@@ -79,6 +79,8 @@ <h2 id="A">A</h2>
       <li><a href="metadata.html#gen3.metadata.Gen3Metadata.async_delete_alias">async_delete_alias() (gen3.metadata.Gen3Metadata method)</a>
 </li>
       <li><a href="metadata.html#gen3.metadata.Gen3Metadata.async_delete_aliases">async_delete_aliases() (gen3.metadata.Gen3Metadata method)</a>
+</li>
+      <li><a href="file.html#gen3.file.Gen3File.async_download_multiple">async_download_multiple() (gen3.file.Gen3File method)</a>
 </li>
       <li><a href="tools/indexing.html#gen3.tools.indexing.download_manifest.async_download_object_manifest">async_download_object_manifest() (in module gen3.tools.indexing.download_manifest)</a>
 </li>
@@ -87,11 +89,11 @@ <h2 id="A">A</h2>
       <li><a href="metadata.html#gen3.metadata.Gen3Metadata.async_get_aliases">async_get_aliases() (gen3.metadata.Gen3Metadata method)</a>
 </li>
       <li><a href="indexing.html#gen3.index.Gen3Index.async_get_record">async_get_record() (gen3.index.Gen3Index method)</a>
-</li>
-      <li><a href="indexing.html#gen3.index.Gen3Index.async_get_records_from_checksum">async_get_records_from_checksum() (gen3.index.Gen3Index method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="indexing.html#gen3.index.Gen3Index.async_get_records_from_checksum">async_get_records_from_checksum() (gen3.index.Gen3Index method)</a>
+</li>
       <li><a href="indexing.html#gen3.index.Gen3Index.async_get_records_on_page">async_get_records_on_page() (gen3.index.Gen3Index method)</a>
 </li>
       <li><a href="indexing.html#gen3.index.Gen3Index.async_get_with_params">async_get_with_params() (gen3.index.Gen3Index method)</a>
@@ -352,10 +354,10 @@ <h2 id="G">G</h2>
 </li>
       <li><a href="submission.html#gen3.submission.Gen3Submission.get_dictionary_all">get_dictionary_all() (gen3.submission.Gen3Submission method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="submission.html#gen3.submission.Gen3Submission.get_dictionary_node">get_dictionary_node() (gen3.submission.Gen3Submission method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="tools/drs_pull.html#gen3.tools.download.drs_download.DownloadManager.get_fresh_token">get_fresh_token() (gen3.tools.download.drs_download.DownloadManager method)</a>
 </li>
       <li><a href="submission.html#gen3.submission.Gen3Submission.get_graphql_schema">get_graphql_schema() (gen3.submission.Gen3Submission method)</a>
@@ -369,6 +371,8 @@ <h2 id="G">G</h2>
       <li><a href="jobs.html#gen3.jobs.Gen3Jobs.get_output">get_output() (gen3.jobs.Gen3Jobs method)</a>
 </li>
       <li><a href="file.html#gen3.file.Gen3File.get_presigned_url">get_presigned_url() (gen3.file.Gen3File method)</a>
+</li>
+      <li><a href="file.html#gen3.file.Gen3File.get_presigned_urls_batch">get_presigned_urls_batch() (gen3.file.Gen3File method)</a>
 </li>
       <li><a href="submission.html#gen3.submission.Gen3Submission.get_programs">get_programs() (gen3.submission.Gen3Submission method)</a>
 </li>

docs/_build/html/index.html

@@ -50,10 +50,12 @@ <h1>Welcome to Gen3 SDK’s documentation!<a class="headerlink" href="#welcome-t
 </li>
 <li class="toctree-l1"><a class="reference internal" href="file.html">Gen3 File Class</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="file.html#gen3.file.Gen3File"><code class="docutils literal notranslate"><span class="pre">Gen3File</span></code></a><ul>
+<li class="toctree-l3"><a class="reference internal" href="file.html#gen3.file.Gen3File.async_download_multiple"><code class="docutils literal notranslate"><span class="pre">Gen3File.async_download_multiple()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="file.html#gen3.file.Gen3File.delete_file"><code class="docutils literal notranslate"><span class="pre">Gen3File.delete_file()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="file.html#gen3.file.Gen3File.delete_file_locations"><code class="docutils literal notranslate"><span class="pre">Gen3File.delete_file_locations()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="file.html#gen3.file.Gen3File.download_single"><code class="docutils literal notranslate"><span class="pre">Gen3File.download_single()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="file.html#gen3.file.Gen3File.get_presigned_url"><code class="docutils literal notranslate"><span class="pre">Gen3File.get_presigned_url()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="file.html#gen3.file.Gen3File.get_presigned_urls_batch"><code class="docutils literal notranslate"><span class="pre">Gen3File.get_presigned_urls_batch()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="file.html#gen3.file.Gen3File.upload_file"><code class="docutils literal notranslate"><span class="pre">Gen3File.upload_file()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="file.html#gen3.file.Gen3File.upload_file_to_guid"><code class="docutils literal notranslate"><span class="pre">Gen3File.upload_file_to_guid()</span></code></a></li>
 </ul>