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<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="#orgc76638c">1. PubSeq REST API</a>
<ul>
<li><a href="#org247cf63">1.1. Introduction</a></li>
<li><a href="#orgcc2b1b0">1.2. Search for an entry</a></li>
<li><a href="#org0ef2d2f">1.3. Fetch metadata</a></li>
<li><a href="#org82c693c">1.4. Fetch EBI XML</a></li>
</ul>
</li>
<li><a href="#org49153e2">2. Configure emacs to run tests</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgc76638c" class="outline-2">
<h2 id="orgc76638c"><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-org247cf63" class="outline-3">
<h3 id="org247cf63"><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
baseURL="http://localhost:5000" # for development
# baseURL="http://covid19.genenetwork.org"
response = requests.get(baseURL+"/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-orgcc2b1b0" class="outline-3">
<h3 id="orgcc2b1b0"><span class="section-number-3">1.2</span> Search for an entry</h3>
<div class="outline-text-3" id="text-1-2">
<p>
When you use the search box on PubSeq it queries the REST end point
for information on the search items. For example
</p>
<div class="org-src-container">
<pre class="src src-python">requests.get(baseURL+"/api/search?s=MT533203.1").json()
</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-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left">collection</td>
<td class="org-left">:</td>
<td class="org-left"><a href="http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126">http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126</a></td>
<td class="org-left">fasta</td>
<td class="org-left">:</td>
<td class="org-left"><a href="http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta">http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta</a></td>
<td class="org-left">id</td>
<td class="org-left">:</td>
<td class="org-left">MT533203.1</td>
<td class="org-left">info</td>
<td class="org-left">:</td>
<td class="org-left"><a href="http://identifiers.org/insdc/MT533203.1#sequence">http://identifiers.org/insdc/MT533203.1#sequence</a></td>
</tr>
</tbody>
</table>
<p>
where collection is the raw uploaded data. The hash value in <code>c=</code> is
computed on the contents of the Arvados keep <a href="https://doc.arvados.org/v2.0/user/tutorials/tutorial-keep-mount-gnu-linux.html">collection</a> and effectively
acts as a deduplication uuid.
</p>
</div>
</div>
<div id="outline-container-org0ef2d2f" class="outline-3">
<h3 id="org0ef2d2f"><span class="section-number-3">1.3</span> Fetch metadata</h3>
<div class="outline-text-3" id="text-1-3">
<p>
Using above collection link you can fetch the metadata in JSON as it
was uploaded originally from the SHeX expression, e.g. using
<a href="https://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/">https://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/</a>
</p>
<p>
But better to use the more advanced sample metadata fetcher
because is does a bit more in terms of expansion
</p>
<div class="org-src-container">
<pre class="src src-python">requests.get(baseURL+"/api/sample/MT533203.1.json").json()
</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" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left">collection</td>
<td class="org-left">:</td>
<td class="org-left"><a href="http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126">http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126</a></td>
<td class="org-left">date</td>
<td class="org-left">:</td>
<td class="org-right">2020-04-27</td>
<td class="org-left">fasta</td>
<td class="org-left">:</td>
<td class="org-left"><a href="http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta">http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta</a></td>
<td class="org-left">id</td>
<td class="org-left">:</td>
<td class="org-left">MT533203.1</td>
<td class="org-left">info</td>
<td class="org-left">:</td>
<td class="org-left"><a href="http://identifiers.org/insdc/MT533203.1#sequence">http://identifiers.org/insdc/MT533203.1#sequence</a></td>
<td class="org-left">mapper</td>
<td class="org-left">:</td>
<td class="org-left">minimap v. 2.17</td>
<td class="org-left">sequencer</td>
<td class="org-left">:</td>
<td class="org-left"><a href="http://www.ebi.ac.uk/efo/EFO_0008632">http://www.ebi.ac.uk/efo/EFO_0008632</a></td>
<td class="org-left">specimen</td>
<td class="org-left">:</td>
<td class="org-left"><a href="http://purl.obolibrary.org/obo/NCIT_C155831">http://purl.obolibrary.org/obo/NCIT_C155831</a></td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-org82c693c" class="outline-3">
<h3 id="org82c693c"><span class="section-number-3">1.4</span> Fetch EBI XML</h3>
<div class="outline-text-3" id="text-1-4">
<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(baseURL+"/api/ebi/sample-MT326090.1.xml").text
</pre>
</div>
<pre class="example">
<?xml version="1.0" encoding="UTF-8"?>
<SAMPLE_SET>
<SAMPLE alias="MT326090.1" 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>http://purl.obolibrary.org/obo/OBI_0000759</VALUE>
</SAMPLE_ATTRIBUTE>
<SAMPLE_ATTRIBUTE>
<TAG>collection date</TAG>
<VALUE>2020-03-21</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>http://purl.obolibrary.org/obo/NCIT_C155831</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-org49153e2" class="outline-2">
<h2 id="org49153e2"><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")
(setq org-babel-eval-verbose t)
</pre>
</div>
<p>
To skip confirmations you may also want to set
</p>
<pre class="example">
(setq org-confirm-babel-evaluate nil)
</pre>
<p>
To see output of the inpreter open then <b>Python</b> buffer.
</p>
</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 05:38</small>.
</div>
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