Feat/dpop

.github/workflows/ci.yaml

@@ -20,8 +20,8 @@ jobs:
       matrix:
         # the versions for which we require the CI to pass on PRs can
         # be updated in the repo settings (branch rules)
-        version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+        version: ['3.13']
       fail-fast: false  # run for all versions even if one of them fails
     with:
         python-version: ${{ matrix.version }}
-        poetry-version: '2.2.1' # Max version supported by python 3.9
+        poetry-version: '2.2.1'

.gitignore

@@ -111,6 +111,17 @@ schema.json
 tests/outputs
 *.sq3
 gen3/tools/indexing/tmp/
+gen3tests-*.logs
+
+# nextflow
+.nextflow
+.nextflow.log*
+
+# AI
+.claude
+.serena
+AGENTS.md
+CLAUDE.md
 
 .dccache
 .idea

.pre-commit-config.yaml

@@ -1,17 +1,17 @@
 repos:
 -   repo: git@github.com:Yelp/detect-secrets
-    rev: v1.4.0
+    rev: v1.5.0
     hooks:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
         exclude: '(docs\/_build|poetry.lock)'
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
     -   id: no-commit-to-branch
         args: [--branch, develop, --branch, master, --pattern, release/.*]
 -   repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 26.5.1
     hooks:
     -   id: black
         additional_dependencies: ['click==8.0.4']

README.md

@@ -9,18 +9,19 @@ The docs here contain general descriptions of the different pieces of the SDK an
 
 * [Detailed API Documentation](https://uc-cdis.github.io/gen3sdk-python/_build/html/index.html)
 
-
 ## Prerequisites
 
 This project is built with Python. Ensure you have Python 3.6 or later installed.
 
 Other prerequisites include:
+
 - [pip](https://pip.pypa.io/en/stable/)
 - Access to a Gen3 commons.
 
 ## Installation Steps:
 
 ### Using pip
+
 To install the latest released version of the SDK, run:
 
 ```
@@ -41,9 +42,10 @@ Additional documentation for different components is available:
 - [Available Classes](docs/reference/sdkClasses.md)
 - [Indexing Tools](docs/howto/diirmIndexing.md)
 - [Metadata Tools](docs/howto/metadataTools.md)
-  - [Gen3 Discovery Page Metadata Tools](docs/howto/discoveryMetadataTools.md)
-  - [Gen3 Subject-level Crosswalk Metadata Tools](docs/howto/crosswalk.md)
+    - [Gen3 Discovery Page Metadata Tools](docs/howto/discoveryMetadataTools.md)
+    - [Gen3 Subject-level Crosswalk Metadata Tools](docs/howto/crosswalk.md)
 - [Bundle Tools](docs/howto/bundleTools.md)
+- [Nextflow with the Gen3 DPoP Proxy](docs/howto/nextflow.md)
 - [Development](docs/howto/devTest.md)
 - [CLI](docs/howto/cli.md)
 
@@ -55,4 +57,4 @@ For FAQs and commonly encountered errors, consult the documentation or use the C
 gen3 --help
 ```
 
-If you encounter issues, raise them on the [Gen3 SDK GitHub Issues page](https://github.com/uc-cdis/gen3sdk-python/issues).
+If you encounter issues, raise them on the [Gen3 SDK GitHub Issues page](https://github.com/uc-cdis/gen3sdk-python/issues).

docs/_build/html/_modules/gen3/auth.html

@@ -104,7 +104,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 <span class="sd">    """</span>
     <span class="n">endpoint</span> <span class="o">=</span> <span class="n">endpoint_from_token</span><span class="p">(</span><span class="n">api_key</span><span class="p">[</span><span class="s2">"api_key"</span><span class="p">])</span>
     <span class="c1"># attempt to get a token from Fence</span>
-    <span class="n">auth_url</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/user/credentials/cdis/access_token"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">endpoint</span><span class="p">)</span>
+    <span class="n">auth_url</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/user/credentials/api/access_token"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">endpoint</span><span class="p">)</span>
     <span class="n">resp</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">post</span><span class="p">(</span><span class="n">auth_url</span><span class="p">,</span> <span class="n">json</span><span class="o">=</span><span class="n">api_key</span><span class="p">)</span>
     <span class="n">token_key</span> <span class="o">=</span> <span class="s2">"access_token"</span>
     <span class="k">return</span> <span class="n">_handle_access_token_response</span><span class="p">(</span><span class="n">resp</span><span class="p">,</span> <span class="n">token_key</span><span class="p">)</span>
@@ -486,6 +486,19 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_access_token</span></div>
 
 
+<div class="viewcode-block" id="Gen3Auth.get_api_key">
+<a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth.get_api_key">[docs]</a>
+    <span class="k">def</span><span class="w"> </span><span class="nf">get_api_key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">"""</span>
+<span class="sd">        Returns the actual API key loaded, or None if the loaded credentials</span>
+<span class="sd">        do not contain one (for example a raw access token).</span>
+<span class="sd">        """</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_refresh_token</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">None</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_refresh_token</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"api_key"</span><span class="p">)</span></div>
+
+
     <span class="k">def</span><span class="w"> </span><span class="nf">_get_auth_value</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">"""Returns the Authorization header value for the request</span>
 

docs/_build/html/auth.html

@@ -124,6 +124,13 @@ <h1>Gen3 Auth Helper<a class="headerlink" href="#gen3-auth-helper" title="Link t
 in the given namespace.  If idp is not set, then default to “local”</p>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="gen3.auth.Gen3Auth.get_api_key">
+<span class="sig-name descname"><span class="pre">get_api_key</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/gen3/auth.html#Gen3Auth.get_api_key"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.auth.Gen3Auth.get_api_key" title="Link to this definition">¶</a></dt>
+<dd><p>Returns the actual API key loaded, or None if the loaded credentials
+do not contain one (for example a raw access token).</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="gen3.auth.Gen3Auth.refresh_access_token">
 <span class="sig-name descname"><span class="pre">refresh_access_token</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">endpoint</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/auth.html#Gen3Auth.refresh_access_token"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.auth.Gen3Auth.refresh_access_token" title="Link to this definition">¶</a></dt>
@@ -173,6 +180,7 @@ <h1 class="logo"><a href="index.html">Gen3 SDK</a></h1>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.auth.Gen3Auth.curl"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.curl()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.auth.Gen3Auth.get_access_token"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.get_access_token()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.auth.Gen3Auth.get_access_token_from_wts"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.get_access_token_from_wts()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#gen3.auth.Gen3Auth.get_api_key"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.get_api_key()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#gen3.auth.Gen3Auth.refresh_access_token"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.refresh_access_token()</span></code></a></li>
 </ul>
 </li>

docs/_build/html/genindex.html

@@ -349,6 +349,8 @@ <h2 id="G">G</h2>
       <li><a href="metadata.html#gen3.metadata.Gen3Metadata.get_aliases">get_aliases() (gen3.metadata.Gen3Metadata method)</a>
 </li>
       <li><a href="indexing.html#gen3.index.Gen3Index.get_all_records">get_all_records() (gen3.index.Gen3Index method)</a>
+</li>
+      <li><a href="auth.html#gen3.auth.Gen3Auth.get_api_key">get_api_key() (gen3.auth.Gen3Auth method)</a>
 </li>
       <li><a href="submission.html#gen3.submission.Gen3Submission.get_dictionary_all">get_dictionary_all() (gen3.submission.Gen3Submission method)</a>
 </li>

docs/_build/html/index.html

@@ -43,6 +43,7 @@ <h1>Welcome to Gen3 SDK’s documentation!<a class="headerlink" href="#welcome-t
 <li class="toctree-l3"><a class="reference internal" href="auth.html#gen3.auth.Gen3Auth.curl"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.curl()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="auth.html#gen3.auth.Gen3Auth.get_access_token"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.get_access_token()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="auth.html#gen3.auth.Gen3Auth.get_access_token_from_wts"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.get_access_token_from_wts()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="auth.html#gen3.auth.Gen3Auth.get_api_key"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.get_api_key()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="auth.html#gen3.auth.Gen3Auth.refresh_access_token"><code class="docutils literal notranslate"><span class="pre">Gen3Auth.refresh_access_token()</span></code></a></li>
 </ul>
 </li>