view env/lib/python3.7/site-packages/planemo/galaxy/ephemeris_sleep.py @ 2:6af9afd405e9 draft

"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
line wrap: on
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#!/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

try:
    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(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()


def sleep(galaxy_url, verbose=False, timeout=0):
    count = 0
    while True:
        try:
            result = requests.get(galaxy_url + '/api/version')
            try:
                result = result.json()
                if verbose:
                    sys.stdout.write("Galaxy Version: %s\n" % result['version_major'])
                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(1)

    return True


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()