Mercurial > repos > gga > apollo_feat_from_gff3

comparison create_or_update_organism.py @ 5:cc098732daf6 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
author gga
date Fri, 31 Aug 2018 09:33:27 -0400
parents 0ab9b5af30e7
children 59904413f3db
comparison
equal deleted inserted replaced
4:7c4a3e737e08 5:cc098732daf6
6 import logging 6 import logging
7 import shutil 7 import shutil
8 import sys 8 import sys
9 import time 9 import time
10 10
11 from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance 11 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
12 logging.basicConfig(level=logging.INFO) 12 logging.basicConfig(level=logging.INFO)
13 log = logging.getLogger(__name__) 13 log = logging.getLogger(__name__)
14
15 14
16 if __name__ == '__main__': 15 if __name__ == '__main__':
17 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance') 16 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
18 WAAuth(parser) 17 WAAuth(parser)
19 18
31 30
32 org_cn = GuessOrg(args, wa) 31 org_cn = GuessOrg(args, wa)
33 if isinstance(org_cn, list): 32 if isinstance(org_cn, list):
34 org_cn = org_cn[0] 33 org_cn = org_cn[0]
35 34
36 # User must have an account 35 # User must have an account, if not, create it
37 gx_user = AssertUser(wa.users.loadUsers(email=args.email)) 36 gx_user = wa.users.assertOrCreateUser(args.email)
38 37
39 log.info("Determining if add or update required") 38 log.info("Determining if add or update required")
40 try: 39 try:
41 org = wa.organisms.findOrganismByCn(org_cn) 40 org = wa.organisms.findOrganismByCn(org_cn)
42 except Exception: 41 except Exception:
43 org = None 42 org = None
44 43
45 if org: 44 if org:
46 has_perms = False
47 old_directory = org['directory'] 45 old_directory = org['directory']
48 for user_owned_organism in gx_user.organismPermissions:
49 if 'WRITE' in user_owned_organism['permissions']:
50 has_perms = True
51 break
52 46
53 if not has_perms: 47 if not PermissionCheck(gx_user, org_cn, "WRITE"):
54 print("Naming Conflict. You do not have permissions to access this organism. Either request permission from the owner, or choose a different name for your organism.") 48 print("Naming Conflict. You do not have permissions to access this organism. Either request permission from the owner, or choose a different name for your organism.")
55 sys.exit(2) 49 sys.exit(2)
56 50
57 log.info("\tUpdating Organism") 51 log.info("\tUpdating Organism")
58 data = wa.organisms.updateOrganismInfo( 52 data = wa.organisms.updateOrganismInfo(