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Merge branch 'master' of github.com:uc-cdis/gen3sdk-python into chore…
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@paulineribeyre
paulineribeyre committed Dec 11, 2020
2 parents d52a02d + 0be25c5 commit a614988
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10 changes: 7 additions & 3 deletions .github/workflows/docs.yml
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Expand Up @@ -22,16 +22,20 @@ jobs:
key: ${{ runner.os }}-poetry-${{ hashFiles(format('{0}{1}', github.workspace, '/poetry.lock')) }}
restore-keys: |
${{ runner.os }}-poetry-
- name: Install dependencies (allow "failures" and attempt to continue)
- name: Install dependencies
run: |
curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -
$HOME/.poetry/bin/poetry install -vv || true
source $HOME/.poetry/env
poetry config virtualenvs.create false
poetry install -vv
sudo apt-get install python3-sphinx
- name: Build docs
run: |
sphinx-build --version
source $HOME/.poetry/env
export PYTHONPATH="${PYTHONPATH}:${{ env.pythonLocation }}/lib/python3.6/site-packages"
cd docs
$HOME/.poetry/bin/poetry run make html
poetry run make html
cd ..
- uses: stefanzweifel/git-auto-commit-action@v4.1.2
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2 changes: 1 addition & 1 deletion docs/_build/html/.buildinfo
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@@ -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: a51d6f20fec2e122738fec3cdcdcdfc5
config: 2f360b63a8d4390c09c4ccdd2b2ab49a
tags: 645f666f9bcd5a90fca523b33c5a78b7
91 changes: 30 additions & 61 deletions docs/_build/html/_modules/gen3/auth.html
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@@ -1,39 +1,45 @@

<!DOCTYPE html>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>gen3.auth &#8212; Gen3 SDK documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
<script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
<script src="../../_static/jquery.js"></script>
<script src="../../_static/underscore.js"></script>
<script src="../../_static/doctools.js"></script>
<script src="../../_static/language_data.js"></script>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../',
VERSION: '',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt'
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />

<link rel="stylesheet" href="../../_static/custom.css" type="text/css" />


<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />

</head><body>
</head>
<body>


<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">


<div class="body" role="main">

<h1>Source code for gen3.auth</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">json</span>
<span class="kn">from</span> <span class="nn">requests.auth</span> <span class="kn">import</span> <span class="n">AuthBase</span>
<span class="kn">from</span> <span class="nn">requests.auth</span> <span class="k">import</span> <span class="n">AuthBase</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">requests</span>

Expand Down Expand Up @@ -66,7 +72,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
<span class="sd"> &gt;&gt;&gt; auth = Gen3Auth()</span>
<span class="sd"> &quot;&quot;&quot;</span>

<span class="k">def</span> <span class="fm">__init__</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="n">refresh_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">refresh_token</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">idp</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">__init__</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="n">refresh_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">refresh_token</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">idp</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_endpoint</span> <span class="o">=</span> <span class="n">endpoint</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_refresh_file</span> <span class="o">=</span> <span class="n">refresh_file</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_refresh_token</span> <span class="o">=</span> <span class="n">refresh_token</span>
Expand Down Expand Up @@ -115,7 +121,7 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
<span class="p">)</span>
<span class="p">)</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="k">def</span> <span class="nf">__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="sd"> This gets called by the python.requests package on outbound requests</span>
Expand Down Expand Up @@ -197,39 +203,10 @@ <h1>Source code for gen3.auth</h1><div class="highlight"><pre>
</pre></div>

</div>

</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h1 class="logo"><a href="../../index.html">Gen3 SDK</a></h1>






<p>
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allowtransparency="true" frameborder="0" scrolling="0" width="200px" height="35px"></iframe>
</p>





<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../auth.html">Gen3 Auth Helper</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../file.html">Gen3 File Class</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../indexing.html">Gen3 Index Class</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../jobs.html">Gen3 Jobs Class</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../metadata.html">Gen3 Metadata Class</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../submission.html">Gen3 Submission Class</a></li>
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Expand All @@ -239,23 +216,15 @@ <h3>Related Topics</h3>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
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<h3>Quick search</h3>
<form class="search" action="../../search.html" method="get">
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<input type="submit" value="Go" />
<div><input type="text" name="q" /></div>
<div><input type="submit" value="Go" /></div>
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87 changes: 28 additions & 59 deletions docs/_build/html/_modules/gen3/file.html
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Original file line number Diff line number Diff line change
@@ -1,34 +1,40 @@

<!DOCTYPE html>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>gen3.file &#8212; Gen3 SDK documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
<script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
<script src="../../_static/jquery.js"></script>
<script src="../../_static/underscore.js"></script>
<script src="../../_static/doctools.js"></script>
<script src="../../_static/language_data.js"></script>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../',
VERSION: '',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt'
};
</script>
<script type="text/javascript" src="../../_static/jquery.js"></script>
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />

<link rel="stylesheet" href="../../_static/custom.css" type="text/css" />


<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />

</head><body>
</head>
<body>


<div class="document">
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<div class="bodywrapper">


<div class="body" role="main">

<h1>Source code for gen3.file</h1><div class="highlight"><pre>
Expand Down Expand Up @@ -60,7 +66,7 @@ <h1>Source code for gen3.file</h1><div class="highlight"><pre>

<span class="sd"> &quot;&quot;&quot;</span>

<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">endpoint</span><span class="p">,</span> <span class="n">auth_provider</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">endpoint</span><span class="p">,</span> <span class="n">auth_provider</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_auth_provider</span> <span class="o">=</span> <span class="n">auth_provider</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_endpoint</span> <span class="o">=</span> <span class="n">endpoint</span>

Expand Down Expand Up @@ -90,39 +96,10 @@ <h1>Source code for gen3.file</h1><div class="highlight"><pre>
</pre></div>

</div>

</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h1 class="logo"><a href="../../index.html">Gen3 SDK</a></h1>






<p>
<iframe src="https://ghbtns.com/github-btn.html?user=uc-cdis&repo=gen3sdk-python&type=watch&count=true&size=large&v=2"
allowtransparency="true" frameborder="0" scrolling="0" width="200px" height="35px"></iframe>
</p>





<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../auth.html">Gen3 Auth Helper</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../file.html">Gen3 File Class</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../indexing.html">Gen3 Index Class</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../jobs.html">Gen3 Jobs Class</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../metadata.html">Gen3 Metadata Class</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../submission.html">Gen3 Submission Class</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../tools.html">Gen3 Tools</a></li>
</ul>

<div class="relations">
<div class="sphinxsidebarwrapper"><div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../../index.html">Documentation overview</a><ul>
Expand All @@ -132,23 +109,15 @@ <h3>Related Topics</h3>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
<div class="searchformwrapper">
<h3>Quick search</h3>
<form class="search" action="../../search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" />
<input type="submit" value="Go" />
<div><input type="text" name="q" /></div>
<div><input type="submit" value="Go" /></div>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
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<script>$('#searchbox').show(0);</script>








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