Merge pull request #194 from uc-cdis/fix/types-missing-from-response

Fix/types missing from response
uc-cdis · Aug 22, 2023 · fcef4ac · fcef4ac
2 parents 36105c1 + 83814f1
commit fcef4ac
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diff --git a/.secrets.baseline b/.secrets.baseline
diff --git a/.travis.yml b/.travis.yml
@@ -13,7 +13,8 @@ jobs:
   - python: 3.10
 before_install:
 - pip install --upgrade pip
-- pip install poetry
+# cannot update poetry to 1.6.x+ until we can update urllib3 >= 2.0.0, see https://github.com/orgs/python-poetry/discussions/8345
+- pip install poetry==1.5.1
 - which poetry
 - poetry --version
 install:

diff --git a/docs/_build/doctrees/auth.doctree b/docs/_build/doctrees/auth.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/file.doctree b/docs/_build/doctrees/file.doctree
diff --git a/docs/_build/doctrees/indexing.doctree b/docs/_build/doctrees/indexing.doctree
diff --git a/docs/_build/doctrees/jobs.doctree b/docs/_build/doctrees/jobs.doctree
diff --git a/docs/_build/doctrees/metadata.doctree b/docs/_build/doctrees/metadata.doctree
diff --git a/docs/_build/doctrees/object.doctree b/docs/_build/doctrees/object.doctree
diff --git a/docs/_build/doctrees/query.doctree b/docs/_build/doctrees/query.doctree
diff --git a/docs/_build/doctrees/submission.doctree b/docs/_build/doctrees/submission.doctree
diff --git a/docs/_build/doctrees/tools.doctree b/docs/_build/doctrees/tools.doctree
diff --git a/docs/_build/doctrees/tools/drs_pull.doctree b/docs/_build/doctrees/tools/drs_pull.doctree
diff --git a/docs/_build/doctrees/tools/indexing.doctree b/docs/_build/doctrees/tools/indexing.doctree
diff --git a/docs/_build/doctrees/tools/metadata.doctree b/docs/_build/doctrees/tools/metadata.doctree
diff --git a/docs/_build/doctrees/wss.doctree b/docs/_build/doctrees/wss.doctree
diff --git a/docs/_build/html/_modules/gen3/auth.html b/docs/_build/html/_modules/gen3/auth.html
@@ -1,15 +1,15 @@
 <!DOCTYPE html>
 
-<html lang="en">
+<html lang="en" data-content_root="../../">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>gen3.auth &#8212; Gen3 SDK  documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=4f649999" />
     <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=039e1c02" />
-    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=b3ba4146"></script>
+    <script src="../../_static/documentation_options.js?v=5929fcd5"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
-    <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
+    <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
@@ -152,7 +152,9 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">cache_prefix</span> <span class="o">+</span> <span class="n">m</span><span class="o">.</span><span class="n">hexdigest</span><span class="p">()</span>
 
 
-<div class="viewcode-block" id="Gen3Auth"><a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth">[docs]</a><span class="k">class</span> <span class="nc">Gen3Auth</span><span class="p">(</span><span class="n">AuthBase</span><span class="p">):</span>
+<div class="viewcode-block" id="Gen3Auth">
+<a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth">[docs]</a>
+<span class="k">class</span> <span class="nc">Gen3Auth</span><span class="p">(</span><span class="n">AuthBase</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Gen3 auth helper class for use with requests auth.</span>
 
 <span class="sd">    Implements requests.auth.AuthBase in order to support JWT authentication.</span>
@@ -386,7 +388,9 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 
         <span class="k">return</span> <span class="n">_response</span>
 
-<div class="viewcode-block" id="Gen3Auth.refresh_access_token"><a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth.refresh_access_token">[docs]</a>    <span class="k">def</span> <span class="nf">refresh_access_token</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">endpoint</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="Gen3Auth.refresh_access_token">
+<a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth.refresh_access_token">[docs]</a>
+    <span class="k">def</span> <span class="nf">refresh_access_token</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">endpoint</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Get a new access token&quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_use_wts</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_access_token</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_access_token_from_wts</span><span class="p">(</span><span class="n">endpoint</span><span class="p">)</span>
@@ -415,6 +419,7 @@ <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>
 
+
     <span class="nd">@backoff</span><span class="o">.</span><span class="n">on_exception</span><span class="p">(</span>
         <span class="n">wait_gen</span><span class="o">=</span><span class="n">backoff</span><span class="o">.</span><span class="n">expo</span><span class="p">,</span> <span class="n">exception</span><span class="o">=</span><span class="ne">Exception</span><span class="p">,</span> <span class="o">**</span><span class="n">DEFAULT_BACKOFF_SETTINGS</span>
     <span class="p">)</span>
@@ -434,7 +439,9 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
             <span class="n">logging</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
             <span class="k">raise</span> <span class="n">e</span>
 
-<div class="viewcode-block" id="Gen3Auth.get_access_token"><a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth.get_access_token">[docs]</a>    <span class="k">def</span> <span class="nf">get_access_token</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="Gen3Auth.get_access_token">
+<a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth.get_access_token">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_access_token</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Get the access token - auto refresh if within 5 minutes of expiration&quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_access_token</span><span class="p">:</span>
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_use_wts</span> <span class="o">==</span> <span class="kc">True</span><span class="p">:</span>
@@ -467,6 +474,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
         <span class="c1"># use cache</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_access_token</span></div>
 
+
     <span class="k">def</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">&quot;&quot;&quot;Returns the Authorization header value for the request</span>
 
@@ -476,7 +484,9 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="s2">&quot;bearer &quot;</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_access_token</span><span class="p">()</span>
 
-<div class="viewcode-block" id="Gen3Auth.curl"><a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth.curl">[docs]</a>    <span class="k">def</span> <span class="nf">curl</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">request</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="Gen3Auth.curl">
+<a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth.curl">[docs]</a>
+    <span class="k">def</span> <span class="nf">curl</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">request</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Curl the given endpoint - ex: gen3 curl /user/user.  Return requests.Response</span>
 
@@ -508,7 +518,10 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Invalid request type: &quot;</span> <span class="o">+</span> <span class="n">request</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">output</span></div>
 
-<div class="viewcode-block" id="Gen3Auth.get_access_token_from_wts"><a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth.get_access_token_from_wts">[docs]</a>    <span class="k">def</span> <span class="nf">get_access_token_from_wts</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">endpoint</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Gen3Auth.get_access_token_from_wts">
+<a class="viewcode-back" href="../../auth.html#gen3.auth.Gen3Auth.get_access_token_from_wts">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_access_token_from_wts</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">endpoint</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Try to fetch an access token for the given idp from the wts</span>
 <span class="sd">        in the given namespace.  If idp is not set, then default to &quot;local&quot;</span>
@@ -651,7 +664,9 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
         <span class="n">err_msg</span> <span class="o">=</span> <span class="s2">&quot;Please make sure the target commons is connected on your profile page and that connection has not expired.&quot;</span>
         <span class="k">if</span> <span class="n">resp</span><span class="o">.</span><span class="n">status_code</span> <span class="o">!=</span> <span class="mi">200</span><span class="p">:</span>
             <span class="n">logging</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="n">err_msg</span><span class="p">)</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="s2">&quot;token&quot;</span><span class="p">)</span></div></div>
+        <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="s2">&quot;token&quot;</span><span class="p">)</span></div>
+</div>
+
 </pre></div>
 
           </div>