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<div id="content">
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgb24ef14">1. PubSeq REST API</a>
<ul>
<li><a href="#orgd7c015d">1.1. Introduction</a></li>
<li><a href="#orgb2caa89">1.2. Fetch EBI XML</a></li>
</ul>
</li>
<li><a href="#org68f26b2">2. Configure emacs to run tests</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgb24ef14" class="outline-2">
<h2 id="orgb24ef14"><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-orgd7c015d" class="outline-3">
<h3 id="orgd7c015d"><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>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-right" />
</colgroup>
<tbody>
<tr>
<td class="org-left">service</td>
<td class="org-left">:</td>
<td class="org-left">PubSeq</td>
<td class="org-left">version</td>
<td class="org-left">:</td>
<td class="org-right">0.1</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-orgb2caa89" class="outline-3">
<h3 id="orgb2caa89"><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>
<pre class="example">
<?xml version="1.0" encoding="UTF-8"?>
<SAMPLE_SET>
<SAMPLE alias="MT32690.1" center_name="COVID-19 PubSeq">
<TITLE>COVID-19 PubSeq Sample</TITLE>
<SAMPLE_NAME>
<TAXON_ID>2697049</TAXON_ID>
<SCIENTIFIC_NAME>Severe acute respiratory syndrome coronavirus 2</SCIENTIFIC_NAME>
<COMMON_NAME>SARS-CoV-2</COMMON_NAME>
</SAMPLE_NAME>
<SAMPLE_ATTRIBUTES>
<SAMPLE_ATTRIBUTE>
<TAG>investigation type</TAG>
<VALUE></VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>sequencing method</TAG>
<VALUE></VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>collection date</TAG>
<VALUE></VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (latitude)</TAG>
<VALUE></VALUE>
<UNITS>DD</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (longitude)</TAG>
<VALUE></VALUE>
<UNITS>DD</UNITS>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (country and/or sea)</TAG>
<VALUE></VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>geographic location (region and locality)</TAG>
<VALUE></VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>environment (material)</TAG>
<VALUE></VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>ENA-CHECKLIST</TAG>
<VALUE>ERC000011</VALUE>
</SAMPLE_ATTRIBUTE>
</SAMPLE_ATTRIBUTES>
</SAMPLE>
</SAMPLE_SET>
</pre>
</div>
</div>
</div>
<div id="outline-container-org68f26b2" class="outline-2">
<h2 id="org68f26b2"><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 06:13</small>.
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