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<body>
<div id="org-div-home-and-up">
 <a accesskey="h" href=""> UP </a>
 |
 <a accesskey="H" href="http://covid19.genenetwork.org/apidoc"> HOME </a>
</div><div id="content">
<h1 class="title">PubSeq REST API</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org0db7287">1. PubSeq REST API</a>
<ul>
<li><a href="#orgd98cd95">1.1. Introduction</a></li>
<li><a href="#org8951ab6">1.2. Fetch EBI XML</a></li>
</ul>
</li>
<li><a href="#orgbde9911">2. Configure emacs to run tests</a></li>
</ul>
</div>
</div>



<div id="outline-container-org0db7287" class="outline-2">
<h2 id="org0db7287"><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-orgd98cd95" class="outline-3">
<h3 id="orgd98cd95"><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-org8951ab6" class="outline-3">
<h3 id="org8951ab6"><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">
&lt;?xml version="1.0" encoding="UTF-8"?&gt;
&lt;SAMPLE_SET&gt;
  &lt;SAMPLE alias="MT32690.1" center_name="COVID-19 PubSeq"&gt;
    &lt;TITLE&gt;COVID-19 PubSeq Sample&lt;/TITLE&gt;
    &lt;SAMPLE_NAME&gt;
      &lt;TAXON_ID&gt;2697049&lt;/TAXON_ID&gt;
      &lt;SCIENTIFIC_NAME&gt;Severe acute respiratory syndrome coronavirus 2&lt;/SCIENTIFIC_NAME&gt;
      &lt;COMMON_NAME&gt;SARS-CoV-2&lt;/COMMON_NAME&gt;
    &lt;/SAMPLE_NAME&gt;
    &lt;SAMPLE_ATTRIBUTES&gt;
      &lt;SAMPLE_ATTRIBUTE&gt;
        &lt;TAG&gt;investigation type&lt;/TAG&gt;
        &lt;VALUE&gt;&lt;/VALUE&gt;
      &lt;/SAMPLE_ATTRIBUTE&gt;
      &lt;SAMPLE_ATTRIBUTE&gt;
        &lt;TAG&gt;sequencing method&lt;/TAG&gt;
        &lt;VALUE&gt;&lt;/VALUE&gt;
      &lt;/SAMPLE_ATTRIBUTE&gt;
      &lt;SAMPLE_ATTRIBUTE&gt;
        &lt;TAG&gt;collection date&lt;/TAG&gt;
        &lt;VALUE&gt;&lt;/VALUE&gt;
      &lt;/SAMPLE_ATTRIBUTE&gt;
      &lt;SAMPLE_ATTRIBUTE&gt;
        &lt;TAG&gt;geographic location (latitude)&lt;/TAG&gt;
        &lt;VALUE&gt;&lt;/VALUE&gt;
     &lt;UNITS&gt;DD&lt;/UNITS&gt;
      &lt;/SAMPLE_ATTRIBUTE&gt;
      &lt;SAMPLE_ATTRIBUTE&gt;
        &lt;TAG&gt;geographic location (longitude)&lt;/TAG&gt;
        &lt;VALUE&gt;&lt;/VALUE&gt;
     &lt;UNITS&gt;DD&lt;/UNITS&gt;
      &lt;/SAMPLE_ATTRIBUTE&gt;
      &lt;SAMPLE_ATTRIBUTE&gt;
     &lt;TAG&gt;geographic location (country and/or sea)&lt;/TAG&gt;
     &lt;VALUE&gt;&lt;/VALUE&gt;
      &lt;/SAMPLE_ATTRIBUTE&gt;
      &lt;SAMPLE_ATTRIBUTE&gt;
        &lt;TAG&gt;geographic location (region and locality)&lt;/TAG&gt;
        &lt;VALUE&gt;&lt;/VALUE&gt;
      &lt;/SAMPLE_ATTRIBUTE&gt;
      &lt;SAMPLE_ATTRIBUTE&gt;
        &lt;TAG&gt;environment (material)&lt;/TAG&gt;
        &lt;VALUE&gt;&lt;/VALUE&gt;
      &lt;/SAMPLE_ATTRIBUTE&gt;
      &lt;SAMPLE_ATTRIBUTE&gt;
        &lt;TAG&gt;ENA-CHECKLIST&lt;/TAG&gt;
        &lt;VALUE&gt;ERC000011&lt;/VALUE&gt;
      &lt;/SAMPLE_ATTRIBUTE&gt;
    &lt;/SAMPLE_ATTRIBUTES&gt;
  &lt;/SAMPLE&gt;
&lt;/SAMPLE_SET&gt;
</pre>
</div>
</div>
</div>

<div id="outline-container-orgbde9911" class="outline-2">
<h2 id="orgbde9911"><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 2020-07-21 Tue 01:32</small>.
</div>
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