Mercurial > repos > gga > apollo_feat_from_gff3
diff fetch_organism_jbrowse.py @ 5:cc098732daf6 draft
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 | 5aa3bc8d0253 |
children | 5d1cf95ade8a |
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--- a/fetch_organism_jbrowse.py Mon Mar 12 06:31:11 2018 -0400 +++ b/fetch_organism_jbrowse.py Fri Aug 31 09:33:27 2018 -0400 @@ -9,7 +9,7 @@ import sys import time -from webapollo import GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance +from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) @@ -55,6 +55,7 @@ WAAuth(parser) OrgOrGuess(parser) parser.add_argument('target_dir', help='Target directory') + parser.add_argument('email', help='User Email') args = parser.parse_args() @@ -65,6 +66,14 @@ org_cn = org_cn[0] org = wa.organisms.findOrganismByCn(org_cn) + # User must have an account, if not, create it + gx_user = wa.users.assertOrCreateUser(args.email) + + # User must have READ access + + if not PermissionCheck(gx_user, org_cn, "READ"): + raise Exception("READ permissions are required for this action") + if not os.path.exists(args.target_dir): os.makedirs(args.target_dir)