Mercurial > repos > gga > apollo_export

comparison fetch_organism_jbrowse.py @ 5:950fb2bf116d 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 09:33:38 -0400
parents b4a85d0c85b8
children c3b5bc8b4080
comparison
equal deleted inserted replaced
4:5559e41721c3 5:950fb2bf116d
7 import os 7 import os
8 import subprocess 8 import subprocess
9 import sys 9 import sys
10 import time 10 import time
11 11
12 from webapollo import GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance 12 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
13 logging.basicConfig(level=logging.INFO) 13 logging.basicConfig(level=logging.INFO)
14 log = logging.getLogger(__name__) 14 log = logging.getLogger(__name__)
15 15
16 16
17 def are_dir_trees_equal(dir1, dir2): 17 def are_dir_trees_equal(dir1, dir2):
53 if __name__ == '__main__': 53 if __name__ == '__main__':
54 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') 54 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
55 WAAuth(parser) 55 WAAuth(parser)
56 OrgOrGuess(parser) 56 OrgOrGuess(parser)
57 parser.add_argument('target_dir', help='Target directory') 57 parser.add_argument('target_dir', help='Target directory')
58 parser.add_argument('email', help='User Email')
58 59
59 args = parser.parse_args() 60 args = parser.parse_args()
60 61
61 wa = WebApolloInstance(args.apollo, args.username, args.password) 62 wa = WebApolloInstance(args.apollo, args.username, args.password)
62 # User must have an account 63 # User must have an account
63 org_cn = GuessOrg(args, wa) 64 org_cn = GuessOrg(args, wa)
64 if isinstance(org_cn, list): 65 if isinstance(org_cn, list):
65 org_cn = org_cn[0] 66 org_cn = org_cn[0]
66 org = wa.organisms.findOrganismByCn(org_cn) 67 org = wa.organisms.findOrganismByCn(org_cn)
68
69 # User must have an account, if not, create it
70 gx_user = wa.users.assertOrCreateUser(args.email)
71
72 # User must have READ access
73
74 if not PermissionCheck(gx_user, org_cn, "READ"):
75 raise Exception("READ permissions are required for this action")
67 76
68 if not os.path.exists(args.target_dir): 77 if not os.path.exists(args.target_dir):
69 os.makedirs(args.target_dir) 78 os.makedirs(args.target_dir)
70 79
71 if not os.path.exists(os.path.join(org['directory'], 'seq')): 80 if not os.path.exists(os.path.join(org['directory'], 'seq')):