Mercurial > repos > eric-rasche > apollo

annotate fetch_organism_jbrowse.py @ 7:f9a6e151b3b4 draft

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
author eric-rasche
date Tue, 27 Jun 2017 04:05:17 -0400
parents d4ae83dedb14
children
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
1 #!/usr/bin/env python
7
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
2 from __future__ import print_function
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
3 import os
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
4 import sys
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
5 import time
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
6 import argparse
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
7 import filecmp
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
8 import os.path
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
9 import logging
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
10 import subprocess
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
11 from webapollo import WAAuth, WebApolloInstance, GuessOrg, OrgOrGuess
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
12 logging.basicConfig(level=logging.INFO)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
13 log = logging.getLogger(__name__)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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15
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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16 def are_dir_trees_equal(dir1, dir2):
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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17 """
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
18 Compare two directories recursively. Files in each directory are
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
19 assumed to be equal if their names and contents are equal.
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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parents: 3
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20
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
21 @param dir1: First directory path
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
22 @param dir2: Second directory path
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
23
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
24 @return: True if the directory trees are the same and
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
25 there were no errors while accessing the directories or files,
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
26 False otherwise.
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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28 # http://stackoverflow.com/questions/4187564/recursive-dircmp-compare-two-directories-to-ensure-they-have-the-same-files-and/6681395#6681395
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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29 """
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
31 dirs_cmp = filecmp.dircmp(dir1, dir2)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
32 if len(dirs_cmp.left_only) > 0 or len(dirs_cmp.right_only) > 0 or \
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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33 len(dirs_cmp.funny_files) > 0:
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
34 print(('LEFT', dirs_cmp.left_only))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
35 print(('RIGHT', dirs_cmp.right_only))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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36 print(('FUNNY', dirs_cmp.funny_files))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
37 return False
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
38 (_, mismatch, errors) = filecmp.cmpfiles(
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
39 dir1, dir2, dirs_cmp.common_files, shallow=False)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
40 if len(mismatch) > 0 or len(errors) > 0:
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
41 print(mismatch)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
42 print(errors)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
43 return False
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
44 for common_dir in dirs_cmp.common_dirs:
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
45 new_dir1 = os.path.join(dir1, common_dir)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
46 new_dir2 = os.path.join(dir2, common_dir)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
47 if not are_dir_trees_equal(new_dir1, new_dir2):
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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48 return False
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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49 return True
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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50
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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51
0
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
52 if __name__ == '__main__':
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
53 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
3
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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54 WAAuth(parser)
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
diff changeset
55 OrgOrGuess(parser)
0
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
56 parser.add_argument('target_dir', help='Target directory')
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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57
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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58 args = parser.parse_args()
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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59
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
60 wa = WebApolloInstance(args.apollo, args.username, args.password)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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61 # User must have an account
3
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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62 org_cn = GuessOrg(args, wa)
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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63 if isinstance(org_cn, list):
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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64 org_cn = org_cn[0]
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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65 org = wa.organisms.findOrganismByCn(org_cn)
0
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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66
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parents:
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67 if not os.path.exists(args.target_dir):
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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parents:
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68 os.makedirs(args.target_dir)
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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parents:
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69
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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70 if not os.path.exists(os.path.join(org['directory'], 'seq')):
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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parents: 3
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71 sys.stderr.write("Missing seq directory BEFORE copy")
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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parents: 3
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72 sys.exit(1)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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parents: 3
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73
0
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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parents:
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74 cmd = [
7
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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75 'rsync', '-avr',
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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76 org['directory'].rstrip('/') + '/',
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
77 os.path.join(args.target_dir, 'data', '')
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
78 ]
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
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79 # We run this OBSESSIVELY because my org had a hiccup where the origin
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
80 # (silent) cp -R failed at one point. This caused MANY HEADACHES.
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
81 #
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
82 # Our response is to run this 3 times (in case the issue is temporary),
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
83 # with delays in between. And ensure that we have the correct number of
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
84 # files / folders before and after.
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
85 sys.stderr.write(' '.join(cmd))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
86 sys.stderr.write('\n')
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
87 sys.stderr.write(subprocess.check_output(cmd))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
88 if not are_dir_trees_equal(
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
89 os.path.join(org['directory'].rstrip('/')),
0
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
diff changeset
90 os.path.join(args.target_dir, 'data')
7
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
91 ):
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
92 # Not good
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
93 time.sleep(5)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
94 sys.stderr.write('\n')
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
95 sys.stderr.write(' '.join(cmd))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
96 sys.stderr.write('\n')
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
97 sys.stderr.write(subprocess.check_output(cmd))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
98 if not are_dir_trees_equal(
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
99 os.path.join(org['directory'].rstrip('/'), 'data'),
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
100 os.path.join(args.target_dir, 'data')
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
101 ):
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
102 time.sleep(5)
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
103 sys.stderr.write('\n')
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
104 sys.stderr.write(' '.join(cmd))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
105 sys.stderr.write('\n')
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
106 sys.stderr.write(subprocess.check_output(cmd))
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
107 if not are_dir_trees_equal(
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
108 os.path.join(org['directory'].rstrip('/'), 'data'),
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
109 os.path.join(args.target_dir, 'data')
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
110 ):
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
111 sys.stderr.write('FAILED THREE TIMES TO COPY. SOMETHING IS WRONG WRONG WRONG.')
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 3
diff changeset
112 sys.exit(2)