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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": "my.email@university.edu",
"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