Mercurial > repos > gga > apollo_feat_from_gff3
annotate fetch_organism_jbrowse.py @ 11:1e37bbd4a73b draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 81492a9c8b9e5649a3867bc30afe617a30fb47a1"
author | gga |
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date | Tue, 14 Apr 2020 10:44:32 -0400 |
parents | 5d1cf95ade8a |
children | bb562d95b6cd |
rev | line source |
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5aa3bc8d0253
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 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 from __future__ import print_function |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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3 |
5aa3bc8d0253
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 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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5 import filecmp |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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6 import logging |
5aa3bc8d0253
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 |
5aa3bc8d0253
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 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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9 import sys |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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10 import time |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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11 |
10
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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12 from apollo import accessible_organisms |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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13 from apollo.util import GuessOrg, OrgOrGuess |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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14 |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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15 from arrow.apollo import get_apollo_instance |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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16 |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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17 from webapollo import UserObj, handle_credentials |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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18 |
0
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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19 logging.basicConfig(level=logging.INFO) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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20 log = logging.getLogger(__name__) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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21 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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22 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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23 def are_dir_trees_equal(dir1, dir2): |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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24 """ |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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25 Compare two directories recursively. Files in each directory are |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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26 assumed to be equal if their names and contents are equal. |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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27 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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28 @param dir1: First directory path |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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29 @param dir2: Second directory path |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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30 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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31 @return: True if the directory trees are the same and |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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32 there were no errors while accessing the directories or files, |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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33 False otherwise. |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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34 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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35 # http://stackoverflow.com/questions/4187564/recursive-dircmp-compare-two-directories-to-ensure-they-have-the-same-files-and/6681395#6681395 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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36 """ |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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37 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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38 dirs_cmp = filecmp.dircmp(dir1, dir2) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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39 if len(dirs_cmp.left_only) > 0 or len(dirs_cmp.right_only) > 0 or \ |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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40 len(dirs_cmp.funny_files) > 0: |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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41 print(('LEFT', dirs_cmp.left_only)) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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42 print(('RIGHT', dirs_cmp.right_only)) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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43 print(('FUNNY', dirs_cmp.funny_files)) |
5aa3bc8d0253
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 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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45 (_, mismatch, errors) = filecmp.cmpfiles( |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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46 dir1, dir2, dirs_cmp.common_files, shallow=False) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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47 if len(mismatch) > 0 or len(errors) > 0: |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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48 print(mismatch) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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49 print(errors) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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50 return False |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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51 for common_dir in dirs_cmp.common_dirs: |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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52 new_dir1 = os.path.join(dir1, common_dir) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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53 new_dir2 = os.path.join(dir2, common_dir) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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54 if not are_dir_trees_equal(new_dir1, new_dir2): |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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55 return False |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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56 return True |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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57 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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58 |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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59 if __name__ == '__main__': |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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60 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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61 OrgOrGuess(parser) |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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62 parser.add_argument('target_dir', help='Target directory') |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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63 parser.add_argument('email', help='User Email') |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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64 |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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65 args = parser.parse_args() |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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66 |
10
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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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67 wa = get_apollo_instance() |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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68 # User must have an account |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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69 org_cn = GuessOrg(args, wa) |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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70 if isinstance(org_cn, list): |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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71 org_cn = org_cn[0] |
5aa3bc8d0253
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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72 |
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73 # User must have an account, if not, create it |
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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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74 gx_user = UserObj(**wa.users._assert_or_create_user(args.email)) |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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75 handle_credentials(gx_user) |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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76 |
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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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77 all_orgs = wa.organisms.get_organisms() |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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78 if 'error' in all_orgs: |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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79 all_orgs = [] |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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80 all_orgs = [org['commonName'] for org in all_orgs] |
5d1cf95ade8a
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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81 if org_cn not in all_orgs: |
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82 raise Exception("Could not find organism %s" % org_cn) |
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83 |
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84 # User must have READ access |
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85 orgs = accessible_organisms(gx_user, [org_cn], 'READ') |
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86 if not orgs: |
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87 raise Exception("You do not have write permission on this organism") |
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88 org = wa.organisms.show_organism(org_cn) |
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89 |
0
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90 if not os.path.exists(args.target_dir): |
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91 os.makedirs(args.target_dir) |
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92 |
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93 if not os.path.exists(os.path.join(org['directory'], 'seq')): |
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94 sys.stderr.write("Missing seq directory BEFORE copy") |
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95 sys.exit(1) |
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96 |
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97 cmd = [ |
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98 'rsync', '-avr', |
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99 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 # We run this OBSESSIVELY because my org had a hiccup where the origin |
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103 # (silent) cp -R failed at one point. This caused MANY HEADACHES. |
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104 # |
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105 # Our response is to run this 3 times (in case the issue is temporary), |
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106 # with delays in between. And ensure that we have the correct number of |
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107 # files / folders before and after. |
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108 sys.stderr.write(' '.join(cmd)) |
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109 sys.stderr.write('\n') |
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110 sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding)) |
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111 if not are_dir_trees_equal( |
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112 os.path.join(org['directory'].rstrip('/')), |
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113 os.path.join(args.target_dir, 'data') |
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114 ): |
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115 # Not good |
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116 time.sleep(5) |
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117 sys.stderr.write('\n') |
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118 sys.stderr.write(' '.join(cmd)) |
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119 sys.stderr.write('\n') |
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120 sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding)) |
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121 if not are_dir_trees_equal( |
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122 os.path.join(org['directory'].rstrip('/'), 'data'), |
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123 os.path.join(args.target_dir, 'data') |
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124 ): |
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125 time.sleep(5) |
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126 sys.stderr.write('\n') |
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127 sys.stderr.write(' '.join(cmd)) |
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128 sys.stderr.write('\n') |
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129 sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding)) |
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130 if not are_dir_trees_equal( |
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131 os.path.join(org['directory'].rstrip('/'), 'data'), |
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132 os.path.join(args.target_dir, 'data') |
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133 ): |
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134 sys.stderr.write('FAILED THREE TIMES TO COPY. SOMETHING IS WRONG WRONG WRONG.') |
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135 sys.exit(2) |