Mercurial > repos > gga > apollo_create_account

annotate fetch_organism_jbrowse.py @ 10:a46a509386d3 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 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:50:13 -0500
parents 356b43302b16
children d6f1caebd5a4
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 filecmp
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
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
7 import os
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 subprocess
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
9 import sys
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 time
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
11
10
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
12 from apollo import accessible_organisms
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
13 from apollo.util import GuessOrg, OrgOrGuess
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
14
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
15 from arrow.apollo import get_apollo_instance
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
16
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
17 from webapollo import UserObj, handle_credentials
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
18
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
19 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
20 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
21
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
22
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
23 def are_dir_trees_equal(dir1, dir2):
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
24 """
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
25 Compare two directories recursively. Files in each directory are
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
26 assumed to be equal if their names and contents are equal.
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
27
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
28 @param dir1: First directory path
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
29 @param dir2: Second directory path
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
30
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
31 @return: True if the directory trees are the same and
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
32 there were no errors while accessing the directories or files,
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
33 False otherwise.
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
34
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
35 # http://stackoverflow.com/questions/4187564/recursive-dircmp-compare-two-directories-to-ensure-they-have-the-same-files-and/6681395#6681395
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
36 """
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
37
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
38 dirs_cmp = filecmp.dircmp(dir1, dir2)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
39 if len(dirs_cmp.left_only) > 0 or len(dirs_cmp.right_only) > 0 or \
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
40 len(dirs_cmp.funny_files) > 0:
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
41 print(('LEFT', dirs_cmp.left_only))
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
42 print(('RIGHT', dirs_cmp.right_only))
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
43 print(('FUNNY', dirs_cmp.funny_files))
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
44 return False
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
45 (_, mismatch, errors) = filecmp.cmpfiles(
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
46 dir1, dir2, dirs_cmp.common_files, shallow=False)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
47 if len(mismatch) > 0 or len(errors) > 0:
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
48 print(mismatch)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
49 print(errors)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
50 return False
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
51 for common_dir in dirs_cmp.common_dirs:
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
52 new_dir1 = os.path.join(dir1, common_dir)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
53 new_dir2 = os.path.join(dir2, common_dir)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
54 if not are_dir_trees_equal(new_dir1, new_dir2):
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
55 return False
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
56 return True
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
57
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
58
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
59 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
60 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
61 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
62 parser.add_argument('target_dir', help='Target directory')
5
356b43302b16 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents: 0
diff changeset
63 parser.add_argument('email', help='User 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
64
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
65 args = parser.parse_args()
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
66
10
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
67 wa = get_apollo_instance()
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
68 # User must have an account
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
69 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
70 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
71 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
72
5
356b43302b16 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents: 0
diff changeset
73 # User must have an account, if not, create it
10
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
74 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
75 handle_credentials(gx_user)
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
76
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
77 all_orgs = wa.organisms.get_organisms()
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
78 if 'error' in all_orgs:
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
79 all_orgs = []
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
80 all_orgs = [org['commonName'] for org in all_orgs]
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
81 if org_cn not in all_orgs:
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
82 raise Exception("Could not find organism %s" % org_cn)
5
356b43302b16 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents: 0
diff changeset
83
356b43302b16 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents: 0
diff changeset
84 # User must have READ access
10
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
85 orgs = accessible_organisms(gx_user, [org_cn], 'READ')
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
86 if not orgs:
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
87 raise Exception("You do not have write permission on this organism")
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
88 org = wa.organisms.show_organism(org_cn)
5
356b43302b16 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents: 0
diff changeset
89
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
90 if not os.path.exists(args.target_dir):
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
91 os.makedirs(args.target_dir)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
92
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
93 if not os.path.exists(os.path.join(org['directory'], 'seq')):
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.stderr.write("Missing seq directory BEFORE copy")
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
95 sys.exit(1)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
96
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
97 cmd = [
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
98 'rsync', '-avr',
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['directory'].rstrip('/') + '/',
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
100 os.path.join(args.target_dir, 'data', '')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
101 ]
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
102 # We run this OBSESSIVELY because my org had a hiccup where the origin
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
103 # (silent) cp -R failed at one point. This caused MANY HEADACHES.
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
104 #
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
105 # Our response is to run this 3 times (in case the issue is temporary),
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
106 # with delays in between. And ensure that we have the correct number of
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
107 # files / folders before and after.
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
108 sys.stderr.write(' '.join(cmd))
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
109 sys.stderr.write('\n')
10
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
110 sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding))
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
111 if not are_dir_trees_equal(
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
112 os.path.join(org['directory'].rstrip('/')),
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
113 os.path.join(args.target_dir, 'data')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
114 ):
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
115 # Not good
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
116 time.sleep(5)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
117 sys.stderr.write('\n')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
118 sys.stderr.write(' '.join(cmd))
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
119 sys.stderr.write('\n')
10
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
120 sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding))
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
121 if not are_dir_trees_equal(
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
122 os.path.join(org['directory'].rstrip('/'), 'data'),
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
123 os.path.join(args.target_dir, 'data')
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 time.sleep(5)
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
126 sys.stderr.write('\n')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
127 sys.stderr.write(' '.join(cmd))
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
128 sys.stderr.write('\n')
10
a46a509386d3 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents: 5
diff changeset
129 sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding))
0
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
130 if not are_dir_trees_equal(
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
131 os.path.join(org['directory'].rstrip('/'), 'data'),
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
132 os.path.join(args.target_dir, 'data')
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 sys.stderr.write('FAILED THREE TIMES TO COPY. SOMETHING IS WRONG WRONG WRONG.')
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
135 sys.exit(2)