Merge pull request #190 from uc-cdis/feat/PXP-10777-casc-auth-sdk

feat(PXP-10777): Utils for cascading authorization

Author: k-burt-uch

.gitignore

@@ -116,3 +116,10 @@ object-manifest.csv
 output_manifest.csv
 
 .dccache
+.idea
+# Files generated during pytest
+input.csv
+test_combined_discovery_metadata.tsv
+test_combined_discovery_metadata_exact_match.tsv
+tmp_output_file.csv
+tmp_output_file_info.csv

docs/_build/doctrees/environment.pickle

@@ -230,15 +230,15 @@ <h1>Welcome to Gen3 SDK’s documentation!<a class="headerlink" href="#welcome-t
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="tools/indexing.html">Indexing Tools</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#download">Download</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#module-gen3.tools.indexing.download_manifest">Download</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.CURRENT_DIR"><code class="docutils literal notranslate"><span class="pre">CURRENT_DIR</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE"><code class="docutils literal notranslate"><span class="pre">INDEXD_RECORD_PAGE_SIZE</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS"><code class="docutils literal notranslate"><span class="pre">MAX_CONCURRENT_REQUESTS</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.TMP_FOLDER"><code class="docutils literal notranslate"><span class="pre">TMP_FOLDER</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.async_download_object_manifest"><code class="docutils literal notranslate"><span class="pre">async_download_object_manifest()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#index">Index</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#module-gen3.tools.indexing.index_manifest">Index</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.index_manifest.CURRENT_DIR"><code class="docutils literal notranslate"><span class="pre">CURRENT_DIR</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.index_manifest.GUID"><code class="docutils literal notranslate"><span class="pre">GUID</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.index_manifest.SIZE"><code class="docutils literal notranslate"><span class="pre">SIZE</span></code></a></li>
@@ -252,7 +252,7 @@ <h1>Welcome to Gen3 SDK’s documentation!<a class="headerlink" href="#welcome-t
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.index_manifest.index_object_manifest"><code class="docutils literal notranslate"><span class="pre">index_object_manifest()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#verify">Verify</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#module-gen3.tools.indexing.verify_manifest">Verify</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.verify_manifest.CURRENT_DIR"><code class="docutils literal notranslate"><span class="pre">CURRENT_DIR</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS"><code class="docutils literal notranslate"><span class="pre">MAX_CONCURRENT_REQUESTS</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.verify_manifest.async_verify_object_manifest"><code class="docutils literal notranslate"><span class="pre">async_verify_object_manifest()</span></code></a></li>
@@ -261,7 +261,7 @@ <h1>Welcome to Gen3 SDK’s documentation!<a class="headerlink" href="#welcome-t
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="tools/metadata.html">Metadata Tools</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="tools/metadata.html#ingest">Ingest</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="tools/metadata.html#module-gen3.tools.metadata.ingest_manifest">Ingest</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="tools/metadata.html#gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID"><code class="docutils literal notranslate"><span class="pre">COLUMN_TO_USE_AS_GUID</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/metadata.html#gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT"><code class="docutils literal notranslate"><span class="pre">GUID_TYPE_FOR_INDEXED_FILE_OBJECT</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="tools/metadata.html#gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT"><code class="docutils literal notranslate"><span class="pre">GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT</span></code></a></li>

docs/_build/doctrees/tools/drs_pull.doctree

@@ -87,15 +87,15 @@ <h1>Gen3 Tools<a class="headerlink" href="#gen3-tools" title="Link to this headi
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="tools/indexing.html">Indexing Tools</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tools/indexing.html#download">Download</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="tools/indexing.html#module-gen3.tools.indexing.download_manifest">Download</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.CURRENT_DIR"><code class="docutils literal notranslate"><span class="pre">CURRENT_DIR</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE"><code class="docutils literal notranslate"><span class="pre">INDEXD_RECORD_PAGE_SIZE</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS"><code class="docutils literal notranslate"><span class="pre">MAX_CONCURRENT_REQUESTS</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.TMP_FOLDER"><code class="docutils literal notranslate"><span class="pre">TMP_FOLDER</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.download_manifest.async_download_object_manifest"><code class="docutils literal notranslate"><span class="pre">async_download_object_manifest()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="tools/indexing.html#index">Index</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="tools/indexing.html#module-gen3.tools.indexing.index_manifest">Index</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.index_manifest.CURRENT_DIR"><code class="docutils literal notranslate"><span class="pre">CURRENT_DIR</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.index_manifest.GUID"><code class="docutils literal notranslate"><span class="pre">GUID</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.index_manifest.SIZE"><code class="docutils literal notranslate"><span class="pre">SIZE</span></code></a></li>
@@ -109,7 +109,7 @@ <h1>Gen3 Tools<a class="headerlink" href="#gen3-tools" title="Link to this headi
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.index_manifest.index_object_manifest"><code class="docutils literal notranslate"><span class="pre">index_object_manifest()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="tools/indexing.html#verify">Verify</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="tools/indexing.html#module-gen3.tools.indexing.verify_manifest">Verify</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.verify_manifest.CURRENT_DIR"><code class="docutils literal notranslate"><span class="pre">CURRENT_DIR</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS"><code class="docutils literal notranslate"><span class="pre">MAX_CONCURRENT_REQUESTS</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/indexing.html#gen3.tools.indexing.verify_manifest.async_verify_object_manifest"><code class="docutils literal notranslate"><span class="pre">async_verify_object_manifest()</span></code></a></li>
@@ -118,7 +118,7 @@ <h1>Gen3 Tools<a class="headerlink" href="#gen3-tools" title="Link to this headi
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="tools/metadata.html">Metadata Tools</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tools/metadata.html#ingest">Ingest</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="tools/metadata.html#module-gen3.tools.metadata.ingest_manifest">Ingest</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="tools/metadata.html#gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID"><code class="docutils literal notranslate"><span class="pre">COLUMN_TO_USE_AS_GUID</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/metadata.html#gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT"><code class="docutils literal notranslate"><span class="pre">GUID_TYPE_FOR_INDEXED_FILE_OBJECT</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="tools/metadata.html#gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT"><code class="docutils literal notranslate"><span class="pre">GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT</span></code></a></li>

docs/_build/doctrees/tools/indexing.doctree

@@ -31,9 +31,9 @@
 
           <div class="body" role="main">
 
-  <section id="drs-download-tools">
-<h1>DRS Download Tools<a class="headerlink" href="#drs-download-tools" title="Link to this heading">¶</a></h1>
-<p id="module-gen3.tools.download.drs_download">Module for downloading and listing JSON DRS manifest and DRS objects. The main classes in
+  <section id="module-gen3.tools.download.drs_download">
+<span id="drs-download-tools"></span><h1>DRS Download Tools<a class="headerlink" href="#module-gen3.tools.download.drs_download" title="Link to this heading">¶</a></h1>
+<p>Module for downloading and listing JSON DRS manifest and DRS objects. The main classes in
 this module for downloading DRS objects are DownloadManager and Manifest.</p>
 <blockquote>
 <div><dl>