Mercurial > repos > gga > apollo_create_or_update

annotate delete_organism.py @ 11:7609529caafa draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 81492a9c8b9e5649a3867bc30afe617a30fb47a1"
author gga
date Tue, 14 Apr 2020 10:41:12 -0400
parents d72192ec8e39
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cd595b5d890a planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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4 import argparse
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5 import logging
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6 import os
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8 from apollo import accessible_organisms
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9 from apollo.util import GuessOrg, OrgOrGuess
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11 from arrow.apollo import get_apollo_instance
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13 from webapollo import UserObj, handle_credentials
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15 logging.basicConfig(level=logging.INFO)
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16 log = logging.getLogger(__name__)
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19 def IsRemote():
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20 return 'GALAXY_SHARED_DIR' not in os.environ or len(os.environ['GALAXY_SHARED_DIR'].lower().strip()) == 0
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23 if __name__ == '__main__':
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24 parser = argparse.ArgumentParser(description='Script to completely delete an organism')
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25 parser.add_argument('email', help='User Email')
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26 OrgOrGuess(parser)
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28 args = parser.parse_args()
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30 wa = get_apollo_instance()
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32 # User must have an account
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33 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
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34 handle_credentials(gx_user)
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36 # Get organism
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37 org_cn = GuessOrg(args, wa)
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38 if isinstance(org_cn, list):
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39 org_cn = org_cn[0]
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41 all_orgs = wa.organisms.get_organisms()
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42 if 'error' in all_orgs:
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43 all_orgs = []
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44 all_orgs = [org['commonName'] for org in all_orgs]
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45 if org_cn not in all_orgs:
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46 raise Exception("Could not find organism %s" % org_cn)
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48 orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
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49 if not orgs:
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50 raise Exception("You do not have write permission on this organism")
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51 org = wa.organisms.show_organism(org_cn)
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53 wa.organisms.delete_features(org['id'])
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55 if IsRemote():
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56 print(wa.remote.delete_organism(org['commonName']))
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57 else:
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58 print(wa.organisms.delete_organism(org['id']))