Mercurial > repos > gga > apollo_list_organism
annotate fetch_organism_jbrowse.py @ 6:ce590fe02ba4 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit d9f27b297d9a919471c92b02ecf6cc9554457211
author | gga |
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date | Tue, 30 Oct 2018 04:28:16 -0400 |
parents | a3000d01c04c |
children | bc2b80fc7e30 |
rev | line source |
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1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 #!/usr/bin/env python |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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2 from __future__ import print_function |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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3 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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4 import argparse |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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5 import filecmp |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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6 import logging |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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7 import os |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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8 import subprocess |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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9 import sys |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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10 import time |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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11 |
5
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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12 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance |
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1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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13 logging.basicConfig(level=logging.INFO) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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14 log = logging.getLogger(__name__) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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16 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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17 def are_dir_trees_equal(dir1, dir2): |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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18 """ |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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19 Compare two directories recursively. Files in each directory are |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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20 assumed to be equal if their names and contents are equal. |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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21 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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22 @param dir1: First directory path |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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23 @param dir2: Second directory path |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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24 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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25 @return: True if the directory trees are the same and |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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26 there were no errors while accessing the directories or files, |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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27 False otherwise. |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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28 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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29 # http://stackoverflow.com/questions/4187564/recursive-dircmp-compare-two-directories-to-ensure-they-have-the-same-files-and/6681395#6681395 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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30 """ |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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31 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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32 dirs_cmp = filecmp.dircmp(dir1, dir2) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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33 if len(dirs_cmp.left_only) > 0 or len(dirs_cmp.right_only) > 0 or \ |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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34 len(dirs_cmp.funny_files) > 0: |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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35 print(('LEFT', dirs_cmp.left_only)) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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36 print(('RIGHT', dirs_cmp.right_only)) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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37 print(('FUNNY', dirs_cmp.funny_files)) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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38 return False |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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39 (_, mismatch, errors) = filecmp.cmpfiles( |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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40 dir1, dir2, dirs_cmp.common_files, shallow=False) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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41 if len(mismatch) > 0 or len(errors) > 0: |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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42 print(mismatch) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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43 print(errors) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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44 return False |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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45 for common_dir in dirs_cmp.common_dirs: |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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46 new_dir1 = os.path.join(dir1, common_dir) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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47 new_dir2 = os.path.join(dir2, common_dir) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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48 if not are_dir_trees_equal(new_dir1, new_dir2): |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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49 return False |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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50 return True |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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51 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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52 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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53 if __name__ == '__main__': |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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54 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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55 WAAuth(parser) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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56 OrgOrGuess(parser) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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57 parser.add_argument('target_dir', help='Target directory') |
5
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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58 parser.add_argument('email', help='User Email') |
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1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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59 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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60 args = parser.parse_args() |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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61 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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62 wa = WebApolloInstance(args.apollo, args.username, args.password) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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63 # User must have an account |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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64 org_cn = GuessOrg(args, wa) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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65 if isinstance(org_cn, list): |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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66 org_cn = org_cn[0] |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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67 org = wa.organisms.findOrganismByCn(org_cn) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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68 |
5
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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69 # User must have an account, if not, create it |
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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70 gx_user = wa.users.assertOrCreateUser(args.email) |
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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71 |
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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72 # User must have READ access |
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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73 |
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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74 if not PermissionCheck(gx_user, org_cn, "READ"): |
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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75 raise Exception("READ permissions are required for this action") |
a3000d01c04c
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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76 |
0
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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77 if not os.path.exists(args.target_dir): |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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78 os.makedirs(args.target_dir) |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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79 |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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80 if not os.path.exists(os.path.join(org['directory'], 'seq')): |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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81 sys.stderr.write("Missing seq directory BEFORE copy") |
1f2e360f7554
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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82 sys.exit(1) |
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83 |
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84 cmd = [ |
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85 'rsync', '-avr', |
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86 org['directory'].rstrip('/') + '/', |
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87 os.path.join(args.target_dir, 'data', '') |
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88 ] |
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89 # We run this OBSESSIVELY because my org had a hiccup where the origin |
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90 # (silent) cp -R failed at one point. This caused MANY HEADACHES. |
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91 # |
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92 # Our response is to run this 3 times (in case the issue is temporary), |
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93 # with delays in between. And ensure that we have the correct number of |
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94 # files / folders before and after. |
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95 sys.stderr.write(' '.join(cmd)) |
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96 sys.stderr.write('\n') |
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97 sys.stderr.write(subprocess.check_output(cmd)) |
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98 if not are_dir_trees_equal( |
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99 os.path.join(org['directory'].rstrip('/')), |
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100 os.path.join(args.target_dir, 'data') |
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101 ): |
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102 # Not good |
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103 time.sleep(5) |
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104 sys.stderr.write('\n') |
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105 sys.stderr.write(' '.join(cmd)) |
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106 sys.stderr.write('\n') |
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107 sys.stderr.write(subprocess.check_output(cmd)) |
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108 if not are_dir_trees_equal( |
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109 os.path.join(org['directory'].rstrip('/'), 'data'), |
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110 os.path.join(args.target_dir, 'data') |
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111 ): |
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112 time.sleep(5) |
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113 sys.stderr.write('\n') |
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114 sys.stderr.write(' '.join(cmd)) |
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115 sys.stderr.write('\n') |
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116 sys.stderr.write(subprocess.check_output(cmd)) |
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117 if not are_dir_trees_equal( |
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118 os.path.join(org['directory'].rstrip('/'), 'data'), |
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119 os.path.join(args.target_dir, 'data') |
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120 ): |
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121 sys.stderr.write('FAILED THREE TIMES TO COPY. SOMETHING IS WRONG WRONG WRONG.') |
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122 sys.exit(2) |