annotate planemo/lib/python3.7/site-packages/ephemeris/sleep.py @ 0:d30785e31577 draft

"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"

1 #!/usr/bin/env python
2 '''Utility to do a blocking sleep until a Galaxy instance is responsive.
3 This is useful in docker images, in RUN steps, where one needs to wait
4 for a currently starting Galaxy to be alive, before API requests can be
5 made successfully.
6 
7 The script functions by making repeated requests to
8 ``http(s)://fqdn/api/version``, an API which requires no authentication
9 to access.'''
10 
11 import sys
12 import time
13 from argparse import ArgumentParser
14 
15 import requests
16 from galaxy.util import unicodify
17 
18 from .common_parser import get_common_args
19 
20 
21 def _parser():
22     '''Constructs the parser object'''
23     parent = get_common_args(login_required=False)
24     parser = ArgumentParser(parents=[parent], usage="usage: %(prog)s <options>",
25                             description="Script to sleep and wait for Galaxy to be alive.")
26     parser.add_argument("--timeout",
27                         default=0, type=int,
28                         help="Galaxy startup timeout in seconds. The default value of 0 waits forever")
29     return parser
30 
31 
32 def _parse_cli_options():
33     """
34     Parse command line options, returning `parse_args` from `ArgumentParser`.
35     """
36     parser = _parser()
37     return parser.parse_args()
38 
39 
40 def galaxy_wait(galaxy_url, timeout=600, verbose=False):
41     count = 0
42     while True:
43         try:
44             result = requests.get(galaxy_url + '/api/version')
45             try:
46                 result = result.json()
47                 if verbose:
48                     sys.stdout.write("Galaxy Version: %s\n" % result['version_major'])
49                 break
50             except ValueError:
51                 if verbose:
52                     sys.stdout.write("[%02d] No valid json returned... %s\n" % (count, result.__str__()))
53                     sys.stdout.flush()
54         except requests.exceptions.ConnectionError as e:
55             if verbose:
56                 sys.stdout.write("[%02d] Galaxy not up yet... %s\n" % (count, unicodify(e)[0:100]))
57                 sys.stdout.flush()
58         count += 1
59 
60         # If we cannot talk to galaxy and are over the timeout
61         if timeout != 0 and count > timeout:
62             sys.stderr.write("Failed to contact Galaxy\n")
63             sys.exit(1)
64 
65         time.sleep(1)
66 
67 
68 def main():
69     """
70     Main function
71     """
72     options = _parse_cli_options()
73 
74     galaxy_wait(options.galaxy, options.timeout, options.verbose)
75 
76     sys.exit(0)
77 
78 
79 if __name__ == "__main__":
80     main()