#!/usr/bin/env python
'''Utility to do a blocking sleep until a Galaxy instance is responsive.
This is useful in docker images, in RUN steps, where one needs to wait
for a currently starting Galaxy to be alive, before API requests can be
made successfully.
The script functions by making repeated requests to
``http(s)://fqdn/api/version``, an API which requires no authentication
to access.'''
import sys
import time
from argparse import ArgumentParser
import requests
from .common_parser import get_common_args
def _parser():
'''Constructs the parser object'''
parent = get_common_args(login_required=False)
parser = ArgumentParser(parents=[parent], usage="usage: python %(prog)s <options>",
description="Script to sleep and wait for Galaxy to be alive.")
parser.add_argument("--timeout",
default=0, type=int,
help="Galaxy startup timeout in seconds. The default value of 0 waits forever")
return parser
def _parse_cli_options():
"""
Parse command line options, returning `parse_args` from `ArgumentParser`.
"""
parser = _parser()
return parser.parse_args()
[docs]def main():
"""
Main function
"""
options = _parse_cli_options()
count = 0
while True:
try:
result = requests.get(options.galaxy + '/api/version').json()
if options.verbose:
sys.stdout.write("Galaxy Version: %s\n" % result['version_major'])
break
except requests.exceptions.ConnectionError as e:
if options.verbose:
sys.stdout.write("[%02d] Galaxy not up yet... %s\n" % (count, str(e)[0:100]))
sys.stdout.flush()
count += 1
# If we cannot talk to galaxy and are over the timeout
if options.timeout != 0 and count > options.timeout:
sys.stderr.write("Failed to contact Galaxy\n")
sys.exit(1)
time.sleep(1)
sys.exit(0)
if __name__ == "__main__":
main()