Mercurial > repos > shellac > guppy_basecaller

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

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -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 The script functions by making repeated requests to
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7 ``http(s)://fqdn/api/version``, an API which requires no authentication
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8 to access.'''
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9
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10 import sys
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11 import time
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12 from argparse import ArgumentParser
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13
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14 import requests
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15 from galaxy.util import unicodify
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16
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17 try:
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18 from .common_parser import get_common_args
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19 except ImportError:
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20 # This won't stay in Planemo long, main no longer functional.
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21 get_common_args = None
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22
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23
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24 def _parser():
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25 '''Constructs the parser object'''
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26 parent = get_common_args(login_required=False)
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27 parser = ArgumentParser(parents=[parent], usage="usage: python %(prog)s <options>",
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28 description="Script to sleep and wait for Galaxy to be alive.")
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29 parser.add_argument("--timeout",
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30 default=0, type=int,
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31 help="Galaxy startup timeout in seconds. The default value of 0 waits forever")
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32 return parser
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33
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34
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35 def _parse_cli_options():
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36 """
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37 Parse command line options, returning `parse_args` from `ArgumentParser`.
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38 """
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39 parser = _parser()
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40 return parser.parse_args()
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41
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42
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43 def sleep(galaxy_url, verbose=False, timeout=0):
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44 count = 0
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45 while True:
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46 try:
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47 result = requests.get(galaxy_url + '/api/version')
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48 try:
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49 result = result.json()
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50 if verbose:
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51 sys.stdout.write("Galaxy Version: %s\n" % result['version_major'])
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52 break
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53 except ValueError:
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54 if verbose:
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55 sys.stdout.write("[%02d] No valid json returned... %s\n" % (count, result.__str__()))
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56 sys.stdout.flush()
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57 except requests.exceptions.ConnectionError as e:
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58 if verbose:
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59 sys.stdout.write("[%02d] Galaxy not up yet... %s\n" % (count, unicodify(e)[:100]))
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60 sys.stdout.flush()
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61 count += 1
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62
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63 # If we cannot talk to galaxy and are over the timeout
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64 if timeout != 0 and count > timeout:
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65 sys.stderr.write("Failed to contact Galaxy\n")
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66 return False
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67
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68 time.sleep(1)
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69
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70 return True
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71
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72
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73 def main():
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74 """
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75 Main function
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76 """
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77 options = _parse_cli_options()
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78
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79 galaxy_alive = sleep(galaxy_url=options.galaxy, verbose=options.verbose, timeout=options.timeout)
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80 exit_code = 0 if galaxy_alive else 1
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81 sys.exit(exit_code)
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82
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83
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84 if __name__ == "__main__":
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85 main()