pyEGA uses the EGA REST API to download authorized datasets and files

and is an alternaive to the supplied EgaDemoClient.jar

REQUIREMENTS

Python "requests" module

http://docs.python-requests.org/en/master/

pip3 install requests

First, store your credentials in ~/.ega.json:

{

"username": "[email protected]",

"password": "SuperSecurePasswordIncludes123",

"key": "symmetric_encryption_key"

}

Your username and password are provided to you by EGA.

The symmetric encryption key can be any non-empty value and

is used to encrypt the data before it is transferred over the wire.

You will still need to decrypt using EgaDemoClient.java

If you know the stable identifier of a dataset (EGAD...) or file (EGAF...)

you can fetch it directly with the "fetch" subcommand. Other commands

to look at specific requests or file details are available. These would

mostly apply to aborted downloads, etc., as the "fetch" command executes

a complete (make request -> list request [metadata] -> download request)

workflow automatically. The "fetch" command will also save a copy of the

request metadata as <requestlabelid>.json

TODO

Download metadata package

List metadata when listing authorized datasets

Verify file size and MD5 hash after download

Parallel download streams

BUGS

Files will be overwritten without warning!

pyEGA version 1.0.0

James S. Blachly, MD

usage: pyega.py [-h] [-d]

{datasets,datasetinfo,requests,rmreq,files,fetch} ...

Download from EMBL EBI's EGA (European Genome-phenome Archive

positional arguments:

{datasets,datasetinfo,requests,rmreq,files,fetch}

subcommands

datasets List authorized datasets

datasetinfo List files in a specified dataset

requests List outstanding requests

rmreq Delete (remove) request label

files List files (optionally, for a specific request label)

fetch Fetch a dataset or file

optional arguments:

-h, --help show this help message and exit

-d, --debug Extra debugging messages