Mercurial > repos > gga > apollo_create_account

annotate create_or_update_organism.py @ 7:0d9cb9e56ca0 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 b9143221aee2cd09e1334ee56ff9651550b1797a
author gga
date Fri, 15 Mar 2019 06:05:10 -0400
parents 356b43302b16
children e80d29fd2a33
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f889e757ca93 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
f889e757ca93 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
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
3
f889e757ca93 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
f889e757ca93 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
f889e757ca93 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
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
7 import os
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
8 import shutil
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
9 import subprocess
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
10 import sys
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
11 import tempfile
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
12 import time
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
13
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
14
5
356b43302b16 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents: 3
diff changeset
15 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
16 logging.basicConfig(level=logging.INFO)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
17 log = logging.getLogger(__name__)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
18
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
19
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
20 def IsBlatEnabled():
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
21 if 'BLAT_ENABLED' not in os.environ:
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
22 return False
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
23 value = os.environ['BLAT_ENABLED']
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
24 if value.lower() in ('true', 't', '1'):
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
25 return True
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
26 else:
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
27 return False
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
28
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
29
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
30 if __name__ == '__main__':
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
31 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
32 WAAuth(parser)
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
33 parser.add_argument('jbrowse_src', help='Old JBrowse Data Directory')
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
34 parser.add_argument('jbrowse', help='JBrowse Data Directory')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
35 parser.add_argument('email', help='User Email')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
36 OrgOrGuess(parser)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
37 parser.add_argument('--genus', help='Organism Genus')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
38 parser.add_argument('--species', help='Organism Species')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
39 parser.add_argument('--public', action='store_true', help='Make organism public')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
40 parser.add_argument('--group', help='Give access to a user group')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
41 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory')
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
42 args = parser.parse_args()
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
43 CHUNK_SIZE = 2**20
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
44 blat_db = None
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
45
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
46 # Cleanup if existing
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
47 if(os.path.exists(args.jbrowse)):
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
48 shutil.rmtree(args.jbrowse)
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
49 # Copy files
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
50 shutil.copytree(args.jbrowse_src, args.jbrowse)
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
51
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
52 path_fasta = args.jbrowse + '/seq/genome.fasta'
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
53 path_2bit = args.jbrowse + '/seq/genome.2bit'
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
54
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
55 # Convert fasta if existing
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
56 if(IsBlatEnabled() and os.path.exists(path_fasta)):
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
57 arg = ['faToTwoBit', path_fasta, path_2bit]
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
58 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-twobit-converter-stderr")
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
59 proc = subprocess.Popen(args=arg, shell=False, cwd=args.jbrowse, stderr=tmp_stderr.fileno())
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
60 return_code = proc.wait()
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
61 if return_code:
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
62 tmp_stderr.flush()
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
63 tmp_stderr.seek(0)
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
64 print("Error building index:", file=sys.stderr)
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
65 while True:
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
66 chunk = tmp_stderr.read(CHUNK_SIZE)
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
67 if not chunk:
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
68 break
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
69 sys.stderr.write(chunk)
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
70 sys.exit(return_code)
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
71 blat_db = path_2bit
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
72 tmp_stderr.close()
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
73
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
74 wa = WebApolloInstance(args.apollo, args.username, args.password)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
75
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
76 org_cn = GuessOrg(args, wa)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
77 if isinstance(org_cn, list):
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
78 org_cn = org_cn[0]
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
79
5
356b43302b16 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents: 3
diff changeset
80 # User must have an account, if not, create it
356b43302b16 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents: 3
diff changeset
81 gx_user = wa.users.assertOrCreateUser(args.email)
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
82
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
83 log.info("Determining if add or update required")
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
84 try:
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
85 org = wa.organisms.findOrganismByCn(org_cn)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
86 except Exception:
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
87 org = None
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
88
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
89 if org:
3
b8e4642ef5dd planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
gga
parents: 0
diff changeset
90 old_directory = org['directory']
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
91
5
356b43302b16 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents: 3
diff changeset
92 if not PermissionCheck(gx_user, org_cn, "WRITE"):
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
93 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.")
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
94 sys.exit(2)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
95
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
96 log.info("\tUpdating Organism")
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
97 data = wa.organisms.updateOrganismInfo(
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
98 org['id'],
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
99 org_cn,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
100 args.jbrowse,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
101 # mandatory
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
102 genus=args.genus,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
103 species=args.species,
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
104 public=args.public,
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
105 blatdb=blat_db
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
106 )
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
107 time.sleep(2)
3
b8e4642ef5dd planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
gga
parents: 0
diff changeset
108 if args.remove_old_directory and args.jbrowse != old_directory:
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
109 shutil.rmtree(old_directory)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
110
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
111 data = [wa.organisms.findOrganismById(org['id'])]
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
112
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
113 else:
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
114 # New organism
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
115 log.info("\tAdding Organism")
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
116 data = wa.organisms.addOrganism(
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
117 org_cn,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
118 args.jbrowse,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
119 genus=args.genus,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
120 species=args.species,
7
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
121 public=args.public,
0d9cb9e56ca0 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
gga
parents: 5
diff changeset
122 blatdb=blat_db
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
123 )
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
124
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
125 # Must sleep before we're ready to handle
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
126 time.sleep(2)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
127 log.info("Updating permissions for %s on %s", gx_user, org_cn)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
128 wa.users.updateOrganismPermission(
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
129 gx_user, org_cn,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
130 write=True,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
131 export=True,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
132 read=True,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
133 )
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
134
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
135 # Group access
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
136 if args.group:
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
137 group = wa.groups.loadGroupByName(name=args.group)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
138 res = wa.groups.updateOrganismPermission(group, org_cn,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
139 administrate=False, write=True, read=True,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
140 export=True)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
141
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
142 data = [o for o in data if o['commonName'] == org_cn]
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
143 print(json.dumps(data, indent=2))