Source code for planemo.galaxy.ephemeris_sleep

#!/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 galaxy.util import unicodify

    from .common_parser import get_common_args
except ImportError:
    # This won't stay in Planemo long, main no longer functional.
    get_common_args = None


def _parser():
    """Constructs the parser object"""
    parent = get_common_args(login_required=False)
    parser = ArgumentParser(
        usage="usage: python %(prog)s <options>",
        description="Script to sleep and wait for Galaxy to be alive.",
        "--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]class SleepCondition: def __init__(self): self.sleep = True
[docs] def cancel(self): self.sleep = False
[docs]def sleep(galaxy_url, verbose=False, timeout=0, sleep_condition=None): if sleep_condition is None: sleep_condition = SleepCondition() count = 0 while sleep_condition.sleep: try: result = requests.get(galaxy_url + "/api/version") try: result = result.json() if verbose: sys.stdout.write("Galaxy Version: %s\n" % result["version_major"]) sys.stdout.flush() break except ValueError: if verbose: sys.stdout.write("[%02d] No valid json returned... %s\n" % (count, result.__str__())) sys.stdout.flush() except requests.exceptions.ConnectionError as e: if verbose: sys.stdout.write("[%02d] Galaxy not up yet... %s\n" % (count, unicodify(e)[:100])) sys.stdout.flush() count += 1 # If we cannot talk to galaxy and are over the timeout if timeout != 0 and count > timeout: sys.stderr.write("Failed to contact Galaxy\n") return False time.sleep(DEFAULT_SLEEP_WAIT) return True
[docs]def main(): """ Main function """ options = _parse_cli_options() galaxy_alive = sleep(galaxy_url=options.galaxy, verbose=options.verbose, timeout=options.timeout) exit_code = 0 if galaxy_alive else 1 sys.exit(exit_code)
if __name__ == "__main__": main()