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# C-c C-e h h publish
# C-c ! insert date (use . for active agenda, C-u C-c ! for date+time, C-u C-c . for time)
# C-c C-t task rotate
# RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png
# C-c C-c to run test blocks
#
# This page runs tests and the HTML export doubles as documentation on
# http://covid19.genenetwork.org/apidoc
#+TITLE: PubSeq REST API
#+AUTHOR: Pjotr Prins
#+HTML_LINK_HOME: http://covid19.genenetwork.org/apidoc
# OPTIONS: section-numbers: nil, with-drawers: t
#+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" />
* PubSeq REST API
Here we document the public REST API that comes with PubSeq. The tests
run in emacs [[https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-python.html][org-babel]]. See the bottom of this document for running
the tests inside emacs. See bottom of the page how to run tests.
** Introduction
We built a REST API for COVID-19 PubSeq. The API source code can be
found in [[https://github.com/arvados/bh20-seq-resource/tree/master/bh20simplewebuploader/api.py][api.py]]. To see if the service is up try
#+begin_src sh
curl http://covid19.genenetwork.org/api/version
#+end_src
#+begin_src js
{
"service": "PubSeq",
"version": 0.1
}
#+end_src
The Python3 version is
#+begin_src python :session :exports both
import requests
baseURL="http://localhost:5067" # 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
#+end_src
#+RESULTS:
| service | : | PubSeq | version | : | 0.1 |
** Search for an entry
When you use the search box on PubSeq it queries the REST end point
for information on the search items. For example
#+begin_src python :session :exports both
requests.get(baseURL+"/api/search?s=MT533203.1").json()
#+end_src
#+RESULTS:
| collection | : | http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+126/sequence.fasta | id | : | MT533203.1 | info | : | http://identifiers.org/insdc/MT533203.1#sequence |
where collection is the raw uploaded data. The hash value in ~c=~ is
computed on the contents of the Arvados keep [[https://doc.arvados.org/v2.0/user/tutorials/tutorial-keep-mount-gnu-linux.html][collection]] and effectively
acts as a deduplication uuid.
** Fetch metadata
Using above collection link you can fetch the metadata in JSON as it
was uploaded originally from the SHeX expression, e.g. using
https://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/
But better to use the more advanced sample metadata fetcher
because is does a bit more in terms of expansion
#+begin_src python :session :exports both
requests.get(baseURL+"/api/sample/MT533203.1.json").json()
#+end_src
#+RESULTS:
| collection | : | http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+126 | date | : | 2020-04-27 | fasta | : | http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+126/sequence.fasta | id | : | MT533203.1 | info | : | http://identifiers.org/insdc/MT533203.1#sequence | mapper | : | minimap v. 2.17 | sequencer | : | http://www.ebi.ac.uk/efo/EFO_0008632 | specimen | : | http://purl.obolibrary.org/obo/NCIT_C155831 |
** Fetch EBI XML
PubSeq provides an API that is used to export formats that are
suitable for uploading data to EBI/ENA from our [[http://covid19.genenetwork.org/export][EXPORT]] menu. This is
documented [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6][here]].
#+begin_src python :session :exports both
requests.get(baseURL+"/api/ebi/sample-MT326090.1.xml").text
#+end_src
#+RESULTS:
#+begin_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>
#+end_example
* Configure emacs to run tests
Execute a code block with C-c C-c. You may need to set
#+begin_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)
(setq org-confirm-babel-evaluate nil)
#+end_src
#+RESULTS:
To skip confirmations you may also want to set
: (setq org-confirm-babel-evaluate nil)
To see output of the interpreter open then *Python* buffer.
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