Mercurial > repos > gga > apollo_export
annotate webapollo.py @ 15:b503fe85f261 draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f742b16e6e4c33b9abdb633405298e05760c84b"
author | gga |
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date | Tue, 08 Jun 2021 09:16:01 +0000 |
parents | c3b5bc8b4080 |
children | f6e09a37bc8b |
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b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 from __future__ import print_function |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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3 import argparse |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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4 import collections |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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5 import json |
b4a85d0c85b8
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 |
b4a85d0c85b8
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 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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8 import time |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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9 from abc import abstractmethod |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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10 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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11 import requests |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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12 |
4
5559e41721c3
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
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13 from six.moves.builtins import next |
5559e41721c3
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
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14 from six.moves.builtins import object |
5559e41721c3
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
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15 |
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c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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16 import yaml |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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17 |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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18 logging.getLogger("requests").setLevel(logging.CRITICAL) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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19 log = logging.getLogger() |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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20 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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21 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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22 ############################################# |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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23 # BEGIN IMPORT OF CACHING LIBRARY # |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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24 ############################################# |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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25 # This code is licensed under the MIT # |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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26 # License and is a copy of code publicly # |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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27 # available in rev. # |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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28 # e27332bc82f4e327aedaec17c9b656ae719322ed # |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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29 # of https://github.com/tkem/cachetools/ # |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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30 ############################################# |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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31 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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32 class DefaultMapping(collections.MutableMapping): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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33 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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34 __slots__ = () |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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35 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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36 @abstractmethod |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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37 def __contains__(self, key): # pragma: nocover |
b4a85d0c85b8
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 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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39 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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40 @abstractmethod |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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41 def __getitem__(self, key): # pragma: nocover |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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42 if hasattr(self.__class__, '__missing__'): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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43 return self.__class__.__missing__(self, key) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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44 else: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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45 raise KeyError(key) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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46 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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47 def get(self, key, default=None): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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48 if key in self: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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49 return self[key] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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50 else: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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51 return default |
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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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52 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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53 __marker = object() |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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54 |
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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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55 def pop(self, key, default=__marker): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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56 if key in self: |
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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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57 value = self[key] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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58 del self[key] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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59 elif default is self.__marker: |
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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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60 raise KeyError(key) |
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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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61 else: |
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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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62 value = default |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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63 return value |
b4a85d0c85b8
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 def setdefault(self, key, default=None): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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66 if key in self: |
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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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67 value = self[key] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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68 else: |
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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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69 self[key] = value = default |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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70 return value |
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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 |
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72 |
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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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73 DefaultMapping.register(dict) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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74 |
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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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75 |
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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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76 class _DefaultSize(object): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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77 def __getitem__(self, _): |
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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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78 return 1 |
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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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79 |
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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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80 def __setitem__(self, _, value): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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81 assert value == 1 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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82 |
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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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83 def pop(self, _): |
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84 return 1 |
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85 |
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86 |
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87 class Cache(DefaultMapping): |
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88 """Mutable mapping to serve as a simple cache or cache base class.""" |
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89 |
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90 __size = _DefaultSize() |
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91 |
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92 def __init__(self, maxsize, missing=None, getsizeof=None): |
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93 if missing: |
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94 self.__missing = missing |
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95 if getsizeof: |
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96 self.__getsizeof = getsizeof |
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97 self.__size = dict() |
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98 self.__data = dict() |
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99 self.__currsize = 0 |
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100 self.__maxsize = maxsize |
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101 |
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102 def __repr__(self): |
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103 return '%s(%r, maxsize=%r, currsize=%r)' % ( |
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104 self.__class__.__name__, |
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105 list(self.__data.items()), |
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106 self.__maxsize, |
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107 self.__currsize, |
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108 ) |
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109 |
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110 def __getitem__(self, key): |
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111 try: |
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112 return self.__data[key] |
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113 except KeyError: |
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114 return self.__missing__(key) |
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115 |
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116 def __setitem__(self, key, value): |
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117 maxsize = self.__maxsize |
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118 size = self.getsizeof(value) |
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119 if size > maxsize: |
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120 raise ValueError('value too large') |
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121 if key not in self.__data or self.__size[key] < size: |
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122 while self.__currsize + size > maxsize: |
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123 self.popitem() |
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124 if key in self.__data: |
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125 diffsize = size - self.__size[key] |
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126 else: |
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127 diffsize = size |
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128 self.__data[key] = value |
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129 self.__size[key] = size |
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130 self.__currsize += diffsize |
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131 |
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132 def __delitem__(self, key): |
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133 size = self.__size.pop(key) |
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134 del self.__data[key] |
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135 self.__currsize -= size |
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136 |
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137 def __contains__(self, key): |
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138 return key in self.__data |
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139 |
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140 def __missing__(self, key): |
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141 value = self.__missing(key) |
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142 try: |
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143 self.__setitem__(key, value) |
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144 except ValueError: |
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145 pass # value too large |
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146 return value |
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147 |
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148 def __iter__(self): |
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149 return iter(self.__data) |
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150 |
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151 def __len__(self): |
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152 return len(self.__data) |
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153 |
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154 @staticmethod |
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155 def __getsizeof(value): |
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156 return 1 |
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157 |
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158 @staticmethod |
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159 def __missing(key): |
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160 raise KeyError(key) |
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161 |
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162 @property |
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163 def maxsize(self): |
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164 """The maximum size of the cache.""" |
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165 return self.__maxsize |
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166 |
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167 @property |
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168 def currsize(self): |
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169 """The current size of the cache.""" |
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170 return self.__currsize |
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171 |
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172 def getsizeof(self, value): |
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173 """Return the size of a cache element's value.""" |
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174 return self.__getsizeof(value) |
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175 |
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176 |
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177 class _Link(object): |
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178 |
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179 __slots__ = ('key', 'expire', 'next', 'prev') |
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180 |
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181 def __init__(self, key=None, expire=None): |
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182 self.key = key |
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183 self.expire = expire |
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184 |
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185 def __reduce__(self): |
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186 return _Link, (self.key, self.expire) |
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187 |
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188 def unlink(self): |
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189 next = self.next |
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190 prev = self.prev |
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191 prev.next = next |
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192 next.prev = prev |
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193 |
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194 |
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195 class _Timer(object): |
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196 |
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197 def __init__(self, timer): |
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198 self.__timer = timer |
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199 self.__nesting = 0 |
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200 |
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201 def __call__(self): |
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202 if self.__nesting == 0: |
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203 return self.__timer() |
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204 else: |
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205 return self.__time |
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206 |
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207 def __enter__(self): |
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208 if self.__nesting == 0: |
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209 self.__time = time = self.__timer() |
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210 else: |
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211 time = self.__time |
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212 self.__nesting += 1 |
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213 return time |
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214 |
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215 def __exit__(self, *exc): |
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216 self.__nesting -= 1 |
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217 |
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218 def __reduce__(self): |
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219 return _Timer, (self.__timer,) |
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220 |
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221 def __getattr__(self, name): |
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222 return getattr(self.__timer, name) |
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223 |
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224 |
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225 class TTLCache(Cache): |
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226 """LRU Cache implementation with per-item time-to-live (TTL) value.""" |
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227 |
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228 def __init__(self, maxsize, ttl, timer=time.time, missing=None, |
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229 getsizeof=None): |
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230 Cache.__init__(self, maxsize, missing, getsizeof) |
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231 self.__root = root = _Link() |
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232 root.prev = root.next = root |
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233 self.__links = collections.OrderedDict() |
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234 self.__timer = _Timer(timer) |
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235 self.__ttl = ttl |
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236 |
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237 def __contains__(self, key): |
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238 try: |
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239 link = self.__links[key] # no reordering |
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240 except KeyError: |
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241 return False |
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242 else: |
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243 return not (link.expire < self.__timer()) |
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244 |
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245 def __getitem__(self, key, cache_getitem=Cache.__getitem__): |
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246 try: |
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247 link = self.__getlink(key) |
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248 except KeyError: |
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249 expired = False |
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250 else: |
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251 expired = link.expire < self.__timer() |
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252 if expired: |
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253 return self.__missing__(key) |
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254 else: |
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255 return cache_getitem(self, key) |
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256 |
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257 def __setitem__(self, key, value, cache_setitem=Cache.__setitem__): |
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258 with self.__timer as time: |
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259 self.expire(time) |
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260 cache_setitem(self, key, value) |
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261 try: |
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262 link = self.__getlink(key) |
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263 except KeyError: |
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264 self.__links[key] = link = _Link(key) |
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265 else: |
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266 link.unlink() |
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267 link.expire = time + self.__ttl |
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268 link.next = root = self.__root |
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269 link.prev = prev = root.prev |
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270 prev.next = root.prev = link |
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271 |
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272 def __delitem__(self, key, cache_delitem=Cache.__delitem__): |
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273 cache_delitem(self, key) |
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274 link = self.__links.pop(key) |
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275 link.unlink() |
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276 if link.expire < self.__timer(): |
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277 raise KeyError(key) |
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278 |
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279 def __iter__(self): |
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280 root = self.__root |
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281 curr = root.next |
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282 while curr is not root: |
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283 # "freeze" time for iterator access |
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284 with self.__timer as time: |
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285 if not (curr.expire < time): |
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286 yield curr.key |
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287 curr = curr.next |
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288 |
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289 def __len__(self): |
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290 root = self.__root |
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291 curr = root.next |
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292 time = self.__timer() |
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293 count = len(self.__links) |
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294 while curr is not root and curr.expire < time: |
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295 count -= 1 |
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296 curr = curr.next |
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297 return count |
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298 |
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299 def __setstate__(self, state): |
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300 self.__dict__.update(state) |
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301 root = self.__root |
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302 root.prev = root.next = root |
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303 for link in sorted(self.__links.values(), key=lambda obj: obj.expire): |
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304 link.next = root |
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305 link.prev = prev = root.prev |
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306 prev.next = root.prev = link |
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307 self.expire(self.__timer()) |
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308 |
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309 def __repr__(self, cache_repr=Cache.__repr__): |
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310 with self.__timer as time: |
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311 self.expire(time) |
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312 return cache_repr(self) |
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313 |
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314 @property |
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315 def currsize(self): |
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316 with self.__timer as time: |
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317 self.expire(time) |
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318 return super(TTLCache, self).currsize |
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319 |
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320 @property |
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321 def timer(self): |
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322 """The timer function used by the cache.""" |
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323 return self.__timer |
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324 |
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325 @property |
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326 def ttl(self): |
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327 """The time-to-live value of the cache's items.""" |
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328 return self.__ttl |
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329 |
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330 def expire(self, time=None): |
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331 """Remove expired items from the cache.""" |
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332 if time is None: |
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333 time = self.__timer() |
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334 root = self.__root |
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335 curr = root.next |
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336 links = self.__links |
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337 cache_delitem = Cache.__delitem__ |
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338 while curr is not root and curr.expire < time: |
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339 cache_delitem(self, curr.key) |
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340 del links[curr.key] |
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341 next = curr.next |
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342 curr.unlink() |
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343 curr = next |
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344 |
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345 def clear(self): |
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346 with self.__timer as time: |
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347 self.expire(time) |
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348 Cache.clear(self) |
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349 |
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350 def get(self, *args, **kwargs): |
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351 with self.__timer: |
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352 return Cache.get(self, *args, **kwargs) |
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353 |
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354 def pop(self, *args, **kwargs): |
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355 with self.__timer: |
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356 return Cache.pop(self, *args, **kwargs) |
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357 |
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358 def setdefault(self, *args, **kwargs): |
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359 with self.__timer: |
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360 return Cache.setdefault(self, *args, **kwargs) |
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361 |
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362 def popitem(self): |
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363 """Remove and return the `(key, value)` pair least recently used that |
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364 has not already expired. |
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365 |
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366 """ |
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367 with self.__timer as time: |
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368 self.expire(time) |
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369 try: |
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370 key = next(iter(self.__links)) |
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371 except StopIteration: |
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372 raise KeyError('%s is empty' % self.__class__.__name__) |
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373 else: |
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374 return (key, self.pop(key)) |
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375 |
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376 if hasattr(collections.OrderedDict, 'move_to_end'): |
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377 def __getlink(self, key): |
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378 value = self.__links[key] |
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379 self.__links.move_to_end(key) |
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380 return value |
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381 else: |
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382 def __getlink(self, key): |
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383 value = self.__links.pop(key) |
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384 self.__links[key] = value |
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385 return value |
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386 |
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387 |
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388 ############################################# |
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389 # END IMPORT OF CACHING LIBRARY # |
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390 ############################################# |
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391 |
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392 |
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393 cache = TTLCache( |
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394 100, # Up to 100 items |
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395 5 * 60 # 5 minute cache life |
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396 ) |
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397 userCache = TTLCache( |
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398 2, # Up to 2 items |
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399 60 # 1 minute cache life |
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400 ) |
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401 |
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402 |
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403 class UnknownUserException(Exception): |
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404 pass |
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405 |
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406 |
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407 def WAAuth(parser): |
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408 parser.add_argument('apollo', help='Complete Apollo URL') |
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409 parser.add_argument('username', help='WA Username') |
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410 parser.add_argument('password', help='WA Password') |
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411 |
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412 |
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413 def OrgOrGuess(parser): |
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414 parser.add_argument('--org_json', type=argparse.FileType("r"), help='Apollo JSON output, source for common name') |
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415 parser.add_argument('--org_raw', help='Common Name') |
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416 parser.add_argument('--org_id', help='Organism ID') |
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417 |
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418 |
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|
419 def CnOrGuess(parser): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff
changeset
|
420 OrgOrGuess(parser) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
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421 parser.add_argument('--seq_fasta', type=argparse.FileType("r"), help='Fasta file, IDs used as sequence sources') |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
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422 parser.add_argument('--seq_raw', nargs='*', help='Sequence Names') |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
423 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
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424 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
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425 def AssertUser(user_list): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
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426 if len(user_list) == 0: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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427 raise UnknownUserException() |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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428 elif len(user_list) == 1: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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429 return user_list[0] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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430 else: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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431 raise Exception("Too many users!") |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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432 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
|
433 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
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434 class WebApolloInstance(object): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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435 |
10
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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diff
changeset
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436 def __init__(self): |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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diff
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437 |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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diff
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438 if 'ARROW_GLOBAL_CONFIG_PATH' in os.environ: |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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439 |
10
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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diff
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440 with open(os.environ['ARROW_GLOBAL_CONFIG_PATH'], 'r') as config: |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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diff
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441 conf = yaml.safe_load(config) |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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diff
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442 try: |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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diff
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443 instance_name = conf['__default'] |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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diff
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444 except KeyError: |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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diff
changeset
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445 raise Exception("Unknown Apollo instance and no __default provided") |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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diff
changeset
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446 self.apollo_url = conf[instance_name]['url'] |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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diff
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447 self.username = conf[instance_name]['username'] |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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448 self.password = conf[instance_name]['password'] |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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diff
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449 else: |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
6
diff
changeset
|
450 self.apollo_url = os.environ['GALAXY_WEBAPOLLO_URL'] |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
6
diff
changeset
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451 self.username = os.environ['GALAXY_WEBAPOLLO_USER'] |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
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diff
changeset
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452 self.password = os.environ['GALAXY_WEBAPOLLO_PASSWORD'] |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
parents:
6
diff
changeset
|
453 |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
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454 self.groups = GroupsClient(self) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
455 self.organisms = OrganismsClient(self) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
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456 self.users = UsersClient(self) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
457 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
458 def __str__(self): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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459 return '<WebApolloInstance at %s>' % self.apollo_url |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
460 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
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461 def requireUser(self, email): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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462 cacheKey = 'user-list' |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
463 try: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
|
464 # Get the cached value |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
465 data = userCache[cacheKey] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
466 except KeyError: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
467 # If we hit a key error above, indicating that |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
468 # we couldn't find the key, we'll simply re-request |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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|
469 # the data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
470 data = self.users.loadUsers() |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
471 userCache[cacheKey] = data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
472 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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473 return AssertUser([x for x in data if x.username == email]) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
474 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
|
475 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
476 class GroupObj(object): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
|
477 def __init__(self, **kwargs): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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478 self.name = kwargs['name'] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
479 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
480 if 'id' in kwargs: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
481 self.groupId = kwargs['id'] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
482 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
483 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
484 class UserObj(object): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
485 ROLE_USER = 'USER' |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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486 ROLE_ADMIN = 'ADMIN' |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
487 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
488 def __init__(self, **kwargs): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
489 # Generally expect 'userId', 'firstName', 'lastName', 'username' (email) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
|
490 for attr in kwargs.keys(): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
491 setattr(self, attr, kwargs[attr]) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
492 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
493 if 'groups' in kwargs: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
494 groups = [] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
495 for groupData in kwargs['groups']: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
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496 groups.append(GroupObj(**groupData)) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
|
497 self.groups = groups |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
498 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
|
499 self.__props = kwargs.keys() |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
500 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
501 def __str__(self): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
502 return '<User %s: %s %s <%s>>' % (self.userId, self.firstName, |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
503 self.lastName, self.username) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
504 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
505 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
506 class Client(object): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
507 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
508 def __init__(self, webapolloinstance, **requestArgs): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
509 self._wa = webapolloinstance |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
510 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
511 self.__verify = requestArgs.get('verify', True) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
512 self._requestArgs = requestArgs |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
513 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
514 if 'verify' in self._requestArgs: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
515 del self._requestArgs['verify'] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
516 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
517 def request(self, clientMethod, data, post_params={}, isJson=True): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
518 url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
519 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
520 headers = { |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
521 'Content-Type': 'application/json' |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
522 } |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
523 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
524 data.update({ |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
525 'username': self._wa.username, |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
526 'password': self._wa.password, |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
527 }) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
528 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
529 r = requests.post(url, data=json.dumps(data), headers=headers, |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
530 verify=self.__verify, params=post_params, allow_redirects=False, **self._requestArgs) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
531 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
532 if r.status_code == 200 or r.status_code == 302: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
533 if isJson: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
534 d = r.json() |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
535 if 'username' in d: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
536 del d['username'] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
537 if 'password' in d: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
538 del d['password'] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
539 return d |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
540 else: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
541 return r.text |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
542 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
543 # @see self.body for HTTP response body |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
544 raise Exception("Unexpected response from apollo %s: %s" % |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
545 (r.status_code, r.text)) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
546 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
547 def get(self, clientMethod, get_params): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
548 url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
549 headers = {} |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
550 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
551 r = requests.get(url, headers=headers, verify=self.__verify, |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
552 params=get_params, **self._requestArgs) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
553 if r.status_code == 200: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
554 d = r.json() |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
555 if 'username' in d: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
556 del d['username'] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
557 if 'password' in d: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
558 del d['password'] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
559 return d |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
560 # @see self.body for HTTP response body |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
561 raise Exception("Unexpected response from apollo %s: %s" % |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
562 (r.status_code, r.text)) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
563 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
564 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
565 class GroupsClient(Client): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
566 CLIENT_BASE = '/group/' |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
567 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
568 def loadGroups(self, group=None): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
569 res = self.request('loadGroups', {}) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
570 data = [GroupObj(**x) for x in res] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
571 if group is not None: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
572 data = [x for x in data if x.name == group] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
573 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
574 return data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
575 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
576 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
577 class OrganismsClient(Client): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
578 CLIENT_BASE = '/organism/' |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
579 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
580 def findAllOrganisms(self): |
5
950fb2bf116d
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents:
4
diff
changeset
|
581 orgs = self.request('findAllOrganisms', {}) |
950fb2bf116d
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents:
4
diff
changeset
|
582 if not isinstance(orgs, (list,)): |
950fb2bf116d
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
gga
parents:
4
diff
changeset
|
583 orgs = [] |
950fb2bf116d
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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584 return orgs |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
585 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
586 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
587 class UsersClient(Client): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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588 CLIENT_BASE = '/user/' |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
589 |
10
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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590 def loadUsers(self): |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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591 res = self.request('loadUsers', {}) |
0
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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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|
592 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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593 data = [UserObj(**x) for x in res] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
594 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
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changeset
|
595 return data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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changeset
|
596 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
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changeset
|
597 |
10
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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598 def handle_credentials(user): |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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599 if hasattr(user, 'new_password'): |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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|
600 f = open("Apollo_credentials.txt", "w") |
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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|
601 f.write('Username:\t%s\nPassword:\t%s' % (user.username, user.new_password)) |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
602 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
603 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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604 def accessible_organisms(user, orgs): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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605 permissionMap = { |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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606 x['organism']: x['permissions'] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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607 for x in user.organismPermissions |
6
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit d9f27b297d9a919471c92b02ecf6cc9554457211
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608 if 'WRITE' in x['permissions'] or 'READ' in x['permissions'] or 'ADMINISTRATE' in x['permissions'] or user.role == 'ADMIN' |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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609 } |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
610 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
611 if 'error' in orgs: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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612 raise Exception("Error received from Apollo server: \"%s\"" % orgs['error']) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
613 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
614 return [ |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
615 (org['commonName'], org['id'], False) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
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616 for org in sorted(orgs, key=lambda x: x['commonName']) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
617 if org['commonName'] in permissionMap |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
618 ] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
619 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
620 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
621 def galaxy_list_groups(trans, *args, **kwargs): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
622 email = trans.get_user().email |
10
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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changeset
|
623 wa = WebApolloInstance() |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
624 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
625 # Key for cached data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
626 cacheKey = 'groups-' + email |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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diff
changeset
|
627 # We don't want to trust "if key in cache" because between asking and fetch |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
628 # it might through key error. |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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diff
changeset
|
629 if cacheKey not in cache: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
630 # However if it ISN'T there, we know we're safe to fetch + put in |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
631 # there. |
5
950fb2bf116d
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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diff
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|
632 data = _galaxy_list_groups(wa, *args, **kwargs) |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
633 cache[cacheKey] = data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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diff
changeset
|
634 return data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
635 try: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
636 # The cache key may or may not be in the cache at this point, it |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
637 # /likely/ is. However we take no chances that it wasn't evicted between |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
638 # when we checked above and now, so we reference the object from the |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
639 # cache in preparation to return. |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
640 data = cache[cacheKey] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff
changeset
|
641 return data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
642 except KeyError: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
643 # If access fails due to eviction, we will fail over and can ensure that |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
644 # data is inserted. |
5
950fb2bf116d
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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diff
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|
645 data = _galaxy_list_groups(wa, *args, **kwargs) |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
646 cache[cacheKey] = data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
647 return data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
648 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
649 |
5
950fb2bf116d
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
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|
650 def _galaxy_list_groups(wa, *args, **kwargs): |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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651 # Fetch the groups. |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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652 group_data = [] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
653 for group in wa.groups.loadGroups(): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
654 # Reformat |
2
d1d6d9fdbfbd
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 33ce5bd0cce35a12725b9ef9aed0683f3c41fbf9
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|
655 group_data.append((group.name, group.name, False)) |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
656 return group_data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
657 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff
changeset
|
658 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
659 def galaxy_list_orgs(trans, *args, **kwargs): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
660 email = trans.get_user().email |
10
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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diff
changeset
|
661 wa = WebApolloInstance() |
0
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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changeset
|
662 try: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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|
663 gx_user = wa.requireUser(email) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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changeset
|
664 except UnknownUserException: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
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|
665 return [] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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666 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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667 # Key for cached data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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668 cacheKey = 'orgs-' + email |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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669 if cacheKey not in cache: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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670 data = _galaxy_list_orgs(wa, gx_user, *args, **kwargs) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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671 cache[cacheKey] = data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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672 return data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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673 try: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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674 data = cache[cacheKey] |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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675 return data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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676 except KeyError: |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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677 data = _galaxy_list_orgs(wa, gx_user, *args, **kwargs) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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678 cache[cacheKey] = data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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679 return data |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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680 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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681 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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682 def _galaxy_list_orgs(wa, gx_user, *args, **kwargs): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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683 # Fetch all organisms |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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684 all_orgs = wa.organisms.findAllOrganisms() |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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685 # Figure out which are accessible to the user |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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686 orgs = accessible_organisms(gx_user, all_orgs) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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687 # Return org list |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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688 return orgs |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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689 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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690 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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691 # This is all for implementing the command line interface for testing. |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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692 class obj(object): |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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693 pass |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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694 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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695 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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696 class fakeTrans(object): |
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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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697 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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698 def __init__(self, username): |
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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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699 self.un = username |
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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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700 |
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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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701 def get_user(self): |
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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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702 o = obj() |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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703 o.email = self.un |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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704 return o |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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705 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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706 |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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707 if __name__ == '__main__': |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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708 parser = argparse.ArgumentParser(description='Test access to apollo server') |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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709 parser.add_argument('email', help='Email of user to test') |
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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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710 parser.add_argument('--action', choices=['org', 'group'], default='org', help='Data set to test, fetch a list of groups or orgs known to the requesting user.') |
0
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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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711 args = parser.parse_args() |
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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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712 |
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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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713 trans = fakeTrans(args.email) |
b4a85d0c85b8
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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714 if args.action == 'org': |
10
c3b5bc8b4080
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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715 print(galaxy_list_orgs(trans)) |
0
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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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716 elif args.action == 'group': |
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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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717 print(galaxy_list_groups(trans)) |