Mercurial > repos > gga > apollo_iframe

annotate create_or_update_organism.py @ 3:951ef9b7bafc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
author gga
date Wed, 20 Sep 2017 09:44:39 -0400
parents 99b348a1d355
children 207c1c281360
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
1 #!/usr/bin/env python
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
2 from __future__ import print_function
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
3
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
4 import argparse
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
5 import json
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
6 import logging
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
7 import shutil
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
8 import sys
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
9 import time
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
10
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
11 from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
12 logging.basicConfig(level=logging.INFO)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
13 log = logging.getLogger(__name__)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
14
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
15
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
16 if __name__ == '__main__':
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
17 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
18 WAAuth(parser)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
19
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
20 parser.add_argument('jbrowse', help='JBrowse Data Directory')
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
21 parser.add_argument('email', help='User Email')
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
22 OrgOrGuess(parser)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
23 parser.add_argument('--genus', help='Organism Genus')
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
24 parser.add_argument('--species', help='Organism Species')
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
25 parser.add_argument('--public', action='store_true', help='Make organism public')
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
26 parser.add_argument('--group', help='Give access to a user group')
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
27 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory')
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
28
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
29 args = parser.parse_args()
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
30 wa = WebApolloInstance(args.apollo, args.username, args.password)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
31
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
32 org_cn = GuessOrg(args, wa)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
33 if isinstance(org_cn, list):
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
34 org_cn = org_cn[0]
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
35
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
36 # User must have an account
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
37 gx_user = AssertUser(wa.users.loadUsers(email=args.email))
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
38
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
39 log.info("Determining if add or update required")
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
40 try:
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
41 org = wa.organisms.findOrganismByCn(org_cn)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
42 except Exception:
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
43 org = None
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
44
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
45 if org:
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
46 has_perms = False
3
951ef9b7bafc planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
gga
parents: 0
diff changeset
47 old_directory = org['directory']
0
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
48 for user_owned_organism in gx_user.organismPermissions:
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
49 if 'WRITE' in user_owned_organism['permissions']:
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
50 has_perms = True
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
51 break
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
52
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
53 if not has_perms:
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
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.")
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
55 sys.exit(2)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
56
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
57 log.info("\tUpdating Organism")
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
58 data = wa.organisms.updateOrganismInfo(
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
59 org['id'],
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
60 org_cn,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
61 args.jbrowse,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
62 # mandatory
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
63 genus=args.genus,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
64 species=args.species,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
65 public=args.public
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
66 )
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
67 time.sleep(2)
3
951ef9b7bafc planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
gga
parents: 0
diff changeset
68 if args.remove_old_directory and args.jbrowse != old_directory:
0
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
69 shutil.rmtree(old_directory)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
70
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
71 data = [wa.organisms.findOrganismById(org['id'])]
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
72
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
73 else:
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
74 # New organism
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
75 log.info("\tAdding Organism")
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
76 data = wa.organisms.addOrganism(
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
77 org_cn,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
78 args.jbrowse,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
79 genus=args.genus,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
80 species=args.species,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
81 public=args.public
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
82 )
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
83
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
84 # Must sleep before we're ready to handle
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
85 time.sleep(2)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
86 log.info("Updating permissions for %s on %s", gx_user, org_cn)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
87 wa.users.updateOrganismPermission(
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
88 gx_user, org_cn,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
89 write=True,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
90 export=True,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
91 read=True,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
92 )
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
93
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
94 # Group access
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
95 if args.group:
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
96 group = wa.groups.loadGroupByName(name=args.group)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
97 res = wa.groups.updateOrganismPermission(group, org_cn,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
98 administrate=False, write=True, read=True,
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
99 export=True)
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
100
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
101 data = [o for o in data if o['commonName'] == org_cn]
99b348a1d355 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
102 print(json.dumps(data, indent=2))