EGA python client
Project description
EGA python client - pyEGA3
pyEGA3 uses the EGA REST API to download authorized datasets and files
Currently works only with Python3
REQUIREMENTS:
Python "requests" module
http://docs.python-requests.org/en/master/
pip3 install requests
Firewall Ports
This client makes https calls to the EGA AAI (https://ega.ebi.ac.uk:8443/) and to the EGA Data API (https://ega.ebi.ac.uk:8051). Both ports 8443 and 8051 must be reachable from the location where this client script is run. Otherwise you will experience timeouts.
(e.g. https://ega.ebi.ac.uk:8443/ega-openid-connect-server/, https://ega.ebi.ac.uk:8051/elixir/central/stats/load should not time out).
-------------------------------------------------------------------------
INSTALLATION:
sudo pip3 install pyega3
-------------------------------------------------------------------------
USAGE:
pyega3 [-h] [-d] -cf CREDENTIALS_FILE [-c CONNECTIONS] {datasets,files,fetch} ...
Download from EMBL EBI's EGA (European Genome-phenome Archive)
positional arguments:
{datasets,files,fetch}
subcommands
datasets List authorized datasets
files List files in a specified dataset
fetch Fetch a dataset or file
optional arguments:
-h, --help show this help message and exit
-d, --debug Extra debugging messages
-cf CREDENTIALS_FILE, --credentials-file CREDENTIALS_FILE
JSON file containing credentials
e.g.{'username':'user1','password':'toor'}
-c CONNECTIONS, --connections CONNECTIONS
Download using specified number of connections
-------------------------------------------------------------------------
Credentials file supposed to be in json format e.g:
{
"username": "my.email@domain.edu",
"password": "mypassword",
"client_secret":"AMenuDLjVdVo4BSwi0QD54LL6NeVDEZRzEQUJ7hJOM3g4imDZBHHX0hNfKHPeQIGkskhtCmqAJtt_jm7EKq-rWw"
}
Your username and password are provided to you by EGA.
pyEGA3 uses the EGA REST API to download authorized datasets and files
Currently works only with Python3
REQUIREMENTS:
Python "requests" module
http://docs.python-requests.org/en/master/
pip3 install requests
Firewall Ports
This client makes https calls to the EGA AAI (https://ega.ebi.ac.uk:8443/) and to the EGA Data API (https://ega.ebi.ac.uk:8051). Both ports 8443 and 8051 must be reachable from the location where this client script is run. Otherwise you will experience timeouts.
(e.g. https://ega.ebi.ac.uk:8443/ega-openid-connect-server/, https://ega.ebi.ac.uk:8051/elixir/central/stats/load should not time out).
-------------------------------------------------------------------------
INSTALLATION:
sudo pip3 install pyega3
-------------------------------------------------------------------------
USAGE:
pyega3 [-h] [-d] -cf CREDENTIALS_FILE [-c CONNECTIONS] {datasets,files,fetch} ...
Download from EMBL EBI's EGA (European Genome-phenome Archive)
positional arguments:
{datasets,files,fetch}
subcommands
datasets List authorized datasets
files List files in a specified dataset
fetch Fetch a dataset or file
optional arguments:
-h, --help show this help message and exit
-d, --debug Extra debugging messages
-cf CREDENTIALS_FILE, --credentials-file CREDENTIALS_FILE
JSON file containing credentials
e.g.{'username':'user1','password':'toor'}
-c CONNECTIONS, --connections CONNECTIONS
Download using specified number of connections
-------------------------------------------------------------------------
Credentials file supposed to be in json format e.g:
{
"username": "my.email@domain.edu",
"password": "mypassword",
"client_secret":"AMenuDLjVdVo4BSwi0QD54LL6NeVDEZRzEQUJ7hJOM3g4imDZBHHX0hNfKHPeQIGkskhtCmqAJtt_jm7EKq-rWw"
}
Your username and password are provided to you by EGA.
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