Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/ephemeris/sleep.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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() |