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1. PubSeq REST API
- 1.1. Introduction
- 1.2. Fetch EBI XML
2. Configure emacs to run tests

1 PubSeq REST API

Here we document the public REST API that comes with PubSeq. The tests run in the amazing emacs org-babel. See the bottom of this document for running the tests inside emacs.

1.1 Introduction

We built a REST API for COVID-19 PubSeq. The API source code can be found in api.py. To see if the service is up try

curl http://covid19.genenetwork.org/api/version

{
  "service": "PubSeq",
  "version": 0.1
}

The Python3 version is

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

1.2 Fetch EBI XML

PubSeq provides an API that is used to export formats that are suitable for uploading data to EBI/ENA from our EXPORT menu. This is documented here.

requests.get("http://covid19.genenetwork.org/api/ebi/sample-MT32690.1.xml").text

2 Configure emacs to run tests

Execute a code block with C-c C-c. You may need to set

(org-babel-do-load-languages
 'org-babel-load-languages
 '((python . t)))
(setq org-babel-python-command "python3")

To skip confirmations you may also want to set

(setq org-confirm-babel-evaluate nil)

Table of Contents

1 PubSeq REST API

1.1 Introduction

1.2 Fetch EBI XML

2 Configure emacs to run tests