Merge pull request #169 from uc-cdis/chore/add_tests

PXP-9373: Unit test for diff manifest

Author: MaribelleHGomez

docs/_build/doctrees/environment.pickle

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c204aa2869f9bc5f949a2abce63f0f44
+config: 5f84980db6ce51f04ab25ae1f011fb32
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/doctrees/tools/drs_pull.doctree

@@ -9,9 +9,6 @@
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css" />
     <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-    <script src="../../_static/jquery.js"></script>
-    <script src="../../_static/underscore.js"></script>
-    <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../../_static/doctools.js"></script>
     <script src="../../_static/sphinx_highlight.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
@@ -60,7 +57,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 
 
 <span class="k">def</span> <span class="nf">decode_token</span><span class="p">(</span><span class="n">token_str</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    jq -r &#39;.api_key&#39; &lt; ~/.gen3/qa-covid19.planx-pla.net.json | awk -F . &#39;{ print $2 }&#39; | base64 --decode | jq -r .</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">tokenParts</span> <span class="o">=</span> <span class="n">token_str</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)</span>
@@ -73,7 +70,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 
 
 <span class="k">def</span> <span class="nf">endpoint_from_token</span><span class="p">(</span><span class="n">token_str</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Extract the endpoint from a JWT issue (&quot;iss&quot; property)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">info</span> <span class="o">=</span> <span class="n">decode_token</span><span class="p">(</span><span class="n">token_str</span><span class="p">)</span>
@@ -85,7 +82,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 
 
 <span class="k">def</span> <span class="nf">_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>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Shared helper for both get_access_token_with_key and get_access_token_from_wts</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">err_msg</span> <span class="o">=</span> <span class="s2">&quot;Failed to get an access token from </span><span class="si">{}</span><span class="s2">:</span><span class="se">\n</span><span class="si">{}</span><span class="s2">&quot;</span>
@@ -101,7 +98,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 
 
 <span class="k">def</span> <span class="nf">get_access_token_with_key</span><span class="p">(</span><span class="n">api_key</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Try to fetch an access token given the api key</span>
 <span class="sd">    &quot;&quot;&quot;</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">&quot;api_key&quot;</span><span class="p">])</span>
@@ -113,7 +110,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 
 
 <span class="k">def</span> <span class="nf">get_access_token_with_client_credentials</span><span class="p">(</span><span class="n">endpoint</span><span class="p">,</span> <span class="n">client_credentials</span><span class="p">,</span> <span class="n">scopes</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Try to get an access token from Fence using client credentials</span>
 
 <span class="sd">    Args:</span>
@@ -145,7 +142,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 
 
 <span class="k">def</span> <span class="nf">get_token_cache_file_name</span><span class="p">(</span><span class="n">key</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Compute the path to the access-token cache file&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Compute the path to the access-token cache file&quot;&quot;&quot;</span>
     <span class="n">cache_folder</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">{}</span><span class="s2">/.cache/gen3/&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span><span class="s2">&quot;~&quot;</span><span class="p">))</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">cache_folder</span><span class="p">):</span>
         <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">cache_folder</span><span class="p">)</span>
@@ -157,7 +154,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 
 
 <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="sd">&quot;&quot;&quot;Gen3 auth helper class for use with requests auth.</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>
 <span class="sd">    Generates access tokens from the provided refresh token file or string.</span>
@@ -335,7 +332,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
 
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">_token_info</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Wrapper to fix intermittent errors when the token is being refreshed</span>
 <span class="sd">        and `_access_token_info` == None</span>
 <span class="sd">        &quot;&quot;&quot;</span>
@@ -344,7 +341,7 @@ <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_info</span>
 
     <span class="k">def</span> <span class="fm">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">request</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Adds authorization header to the request</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Adds authorization header to the request</span>
 
 <span class="sd">        This gets called by the python.requests package on outbound requests</span>
 <span class="sd">        so that authentication can be added.</span>
@@ -358,7 +355,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">request</span>
 
     <span class="k">def</span> <span class="nf">_handle_401</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">response</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Handles failed requests when authorization failed.</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Handles failed requests when authorization failed.</span>
 
 <span class="sd">        This gets called after a failed request when an HTTP 401 error</span>
 <span class="sd">        occurs. This then tries to refresh the access token in the event</span>
@@ -387,7 +384,7 @@ <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>
-        <span class="sd">&quot;&quot;&quot;Get a new access token&quot;&quot;&quot;</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>
         <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">_client_credentials</span><span class="p">:</span>
@@ -435,7 +432,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
             <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>
-        <span class="sd">&quot;&quot;&quot;Get the access token - auto refresh if within 5 minutes of expiration&quot;&quot;&quot;</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>
                 <span class="n">cache_file</span> <span class="o">=</span> <span class="n">get_token_cache_file_name</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_wts_idp</span><span class="p">)</span>
@@ -468,7 +465,7 @@ <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="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="sd">&quot;&quot;&quot;Returns the Authorization header value for the request</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Returns the Authorization header value for the request</span>
 
 <span class="sd">        This gets called when added the Authorization header to the request.</span>
 <span class="sd">        This fetches the access token from the refresh token if the access token is missing.</span>
@@ -477,7 +474,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
         <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>
-        <span class="sd">&quot;&quot;&quot;</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>
 
 <span class="sd">        Args:</span>
@@ -509,7 +506,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
         <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>
-        <span class="sd">&quot;&quot;&quot;</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>
 <span class="sd">        &quot;&quot;&quot;</span>