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<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc04a8fc">1. PubSeq REST API</a>
<ul>
<li><a href="#org239717f">1.1. Introduction</a></li>
<li><a href="#org6637383">1.2. Fetch EBI XML</a></li>
</ul>
</li>
<li><a href="#org1577576">2. Configure emacs to run tests</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgc04a8fc" class="outline-2">
<h2 id="orgc04a8fc"><span class="section-number-2">1</span> PubSeq REST API</h2>
<div class="outline-text-2" id="text-1">
<p>
Here we document the public REST API that comes with PubSeq. The tests
run in the amazing emacs <a href="https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-python.html">org-babel</a>. See the bottom of this document
for running the tests inside emacs.
</p>
</div>
<div id="outline-container-org239717f" class="outline-3">
<h3 id="org239717f"><span class="section-number-3">1.1</span> Introduction</h3>
<div class="outline-text-3" id="text-1-1">
<p>
We built a REST API for COVID-19 PubSeq. The API source code can be
found in <a href="https://github.com/arvados/bh20-seq-resource/tree/master/bh20simplewebuploader/api.py">api.py</a>. To see if the service is up try
</p>
<div class="org-src-container">
<pre class="src src-sh">curl http://covid19.genenetwork.org/api/version
</pre>
</div>
<div class="org-src-container">
<pre class="src src-js">{
"service": "PubSeq",
"version": 0.1
}
</pre>
</div>
<p>
The Python3 version is
</p>
<div class="org-src-container">
<pre class="src src-python">import requests
response = requests.get("http://covid19.genenetwork.org/api/version")
response_body = response.json()
assert response_body["service"] == "PubSeq", "PubSeq API not found"
response_body
</pre>
</div>
</div>
</div>
<div id="outline-container-org6637383" class="outline-3">
<h3 id="org6637383"><span class="section-number-3">1.2</span> Fetch EBI XML</h3>
<div class="outline-text-3" id="text-1-2">
<p>
PubSeq provides an API that is used to export formats that are
suitable for uploading data to EBI/ENA from our <a href="http://covid19.genenetwork.org/export">EXPORT</a> menu. This is
documented <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6">here</a>.
</p>
<div class="org-src-container">
<pre class="src src-python">requests.get("http://covid19.genenetwork.org/api/ebi/sample-MT32690.1.xml").text
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-org1577576" class="outline-2">
<h2 id="org1577576"><span class="section-number-2">2</span> Configure emacs to run tests</h2>
<div class="outline-text-2" id="text-2">
<p>
Execute a code
block with C-c C-c. You may need to set
</p>
<div class="org-src-container">
<pre class="src src-elisp">(org-babel-do-load-languages
'org-babel-load-languages
'((python . t)))
(setq org-babel-python-command "python3")
</pre>
</div>
<p>
To skip confirmations you may also want to set
</p>
<pre class="example">
(setq org-confirm-babel-evaluate nil)
</pre>
</div>
</div>
</div>
<div id="postamble" class="status">
<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-20 Mon 06:02</small>.
</div>
</body>
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