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3
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1 #-------------------------
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2 # Export Galaxy history data to a JSON compatible text file
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3 #
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4 # Galaxy host can be retrieved using the GALAXY_HOST environment
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5 # variable
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6 # Galaxy API key can be retrieved using the GALAXY_API_KEY
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7 # environment variable
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8 #-------------------------
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9
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10 from blend.galaxy import GalaxyInstance
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11
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12 import argparse, sys, logging, os, json
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13
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14 LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s'
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15 LOG_DATEFMT = '%Y-%m-%d %H:%M:%S'
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16 LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
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17
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18 def make_parser():
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19 parser = argparse.ArgumentParser(description='Export Galaxy history data')
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20 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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21 help='logging level (default: INFO)', default='INFO')
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22 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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23 parser.add_argument('--galaxy_host', type=str, help='galaxy host (with port)')
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24 parser.add_argument('--api_key', type=str, help='Galaxy API key')
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25 parser.add_argument('--history_id', type=str, required=True,
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26 help='ID fo the history that will be exported')
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27 parser.add_argument('--no_peek', action='store_true',
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28 help='remove preview from datasets details')
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29 parser.add_argument('--ofile', type=str, required=True,
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30 help='output file')
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31 return parser
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32
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33 def check_history_id(galaxy_instance, history_id):
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34 hmap = dict((str(h['id']), str(h['name']))
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35 for h in galaxy_instance.histories.get_histories())
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36 return history_id in hmap
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37
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38 def main(argv):
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39 parser = make_parser()
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40 args = parser.parse_args(argv)
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41
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42 log_level = getattr(logging, args.loglevel)
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43 kwargs = {'format' : LOG_FORMAT,
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44 'datefmt' : LOG_DATEFMT,
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45 'level' : log_level}
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46 if args.logfile:
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47 kwargs['filename'] = args.logfile
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48 logging.basicConfig(**kwargs)
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49 logger = logging.getLogger('history_to_file')
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50
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51 try:
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52 galaxy_host = args.galaxy_host or os.environ['GALAXY_HOST']
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53 api_key = args.api_key or os.environ['GALAXY_API_KEY']
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54 except KeyError, ke:
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55 msg = 'No argument passed and no global variable %s found' % ke
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56 logger.critical(msg)
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57 sys.exit(msg)
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58
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59 logger.info('opening connection to %s' % galaxy_host)
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60 gi = GalaxyInstance(galaxy_host, key=api_key)
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61
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62 if not check_history_id(gi, args.history_id):
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63 msg = 'Unable to find history with ID %s' % args.history_id
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64 logger.critical(msg)
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65 sys.exit(msg)
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66
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67 logger.info('getting data for history %s' % args.history_id)
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68 h_data = gi.histories.get_history_details(args.history_id, args.no_peek)
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69
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70 logger.info('saving to file %s' % args.ofile)
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71 with open(args.ofile, 'w') as out_file:
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72 out_file.write(json.dumps(h_data))
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73 logger.info('Job completed')
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74
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75 if __name__ == '__main__':
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76 main(sys.argv[1:])
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