Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/ephemeris/sleep.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 #!/usr/bin/env python
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2 '''Utility to do a blocking sleep until a Galaxy instance is responsive.
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3 This is useful in docker images, in RUN steps, where one needs to wait
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4 for a currently starting Galaxy to be alive, before API requests can be
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5 made successfully.
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6
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7 The script functions by making repeated requests to
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8 ``http(s)://fqdn/api/version``, an API which requires no authentication
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9 to access.'''
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10
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11 import sys
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12 import time
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13 from argparse import ArgumentParser
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14
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15 import requests
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16 from galaxy.util import unicodify
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17
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18 from .common_parser import get_common_args
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19
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20
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21 def _parser():
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22 '''Constructs the parser object'''
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23 parent = get_common_args(login_required=False)
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24 parser = ArgumentParser(parents=[parent], usage="usage: %(prog)s <options>",
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25 description="Script to sleep and wait for Galaxy to be alive.")
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26 parser.add_argument("--timeout",
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27 default=0, type=int,
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28 help="Galaxy startup timeout in seconds. The default value of 0 waits forever")
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29 return parser
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30
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31
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32 def _parse_cli_options():
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33 """
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34 Parse command line options, returning `parse_args` from `ArgumentParser`.
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35 """
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36 parser = _parser()
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37 return parser.parse_args()
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38
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39
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40 def galaxy_wait(galaxy_url, timeout=600, verbose=False):
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41 count = 0
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42 while True:
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43 try:
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44 result = requests.get(galaxy_url + '/api/version')
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45 try:
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46 result = result.json()
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47 if verbose:
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48 sys.stdout.write("Galaxy Version: %s\n" % result['version_major'])
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49 break
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50 except ValueError:
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51 if verbose:
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52 sys.stdout.write("[%02d] No valid json returned... %s\n" % (count, result.__str__()))
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53 sys.stdout.flush()
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54 except requests.exceptions.ConnectionError as e:
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55 if verbose:
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56 sys.stdout.write("[%02d] Galaxy not up yet... %s\n" % (count, unicodify(e)[0:100]))
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57 sys.stdout.flush()
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58 count += 1
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59
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60 # If we cannot talk to galaxy and are over the timeout
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61 if timeout != 0 and count > timeout:
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62 sys.stderr.write("Failed to contact Galaxy\n")
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63 sys.exit(1)
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64
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65 time.sleep(1)
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66
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67
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68 def main():
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69 """
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70 Main function
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71 """
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72 options = _parse_cli_options()
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73
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74 galaxy_wait(options.galaxy, options.timeout, options.verbose)
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75
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76 sys.exit(0)
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77
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78
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79 if __name__ == "__main__":
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80 main()