Mercurial > repos > gga > chado_organism_add_organism
annotate chado.py @ 9:7b552f5cb694 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 35c5eff77b573a66f3611b4906417df9a440c857
author | gga |
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date | Tue, 05 Mar 2019 05:14:43 -0500 |
parents | ad220cb1ce2b |
children | 6512156f6a17 |
rev | line source |
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0
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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1 import collections |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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2 import os |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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3 import time |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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4 from abc import abstractmethod |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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5 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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6 import chado |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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7 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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8 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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9 ############################################# |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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10 # BEGIN IMPORT OF CACHING LIBRARY # |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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11 ############################################# |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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12 # This code is licensed under the MIT # |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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13 # License and is a copy of code publicly # |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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14 # available in rev. # |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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15 # e27332bc82f4e327aedaec17c9b656ae719322ed # |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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16 # of https://github.com/tkem/cachetools/ # |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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17 ############################################# |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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18 class DefaultMapping(collections.MutableMapping): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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19 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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20 __slots__ = () |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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21 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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22 @abstractmethod |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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23 def __contains__(self, key): # pragma: nocover |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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24 return False |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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25 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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26 @abstractmethod |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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27 def __getitem__(self, key): # pragma: nocover |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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28 if hasattr(self.__class__, '__missing__'): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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29 return self.__class__.__missing__(self, key) |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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30 else: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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31 raise KeyError(key) |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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32 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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33 def get(self, key, default=None): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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34 if key in self: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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35 return self[key] |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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36 else: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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37 return default |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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38 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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39 __marker = object() |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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40 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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41 def pop(self, key, default=__marker): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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42 if key in self: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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43 value = self[key] |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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44 del self[key] |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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45 elif default is self.__marker: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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46 raise KeyError(key) |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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47 else: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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48 value = default |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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49 return value |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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50 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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51 def setdefault(self, key, default=None): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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52 if key in self: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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53 value = self[key] |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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54 else: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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55 self[key] = value = default |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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56 return value |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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57 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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58 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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59 DefaultMapping.register(dict) |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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60 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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61 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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62 class _DefaultSize(object): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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63 def __getitem__(self, _): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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64 return 1 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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65 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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66 def __setitem__(self, _, value): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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67 assert value == 1 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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68 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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69 def pop(self, _): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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70 return 1 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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71 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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72 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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73 class Cache(DefaultMapping): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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74 """Mutable mapping to serve as a simple cache or cache base class.""" |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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75 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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76 __size = _DefaultSize() |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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77 |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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78 def __init__(self, maxsize, missing=None, getsizeof=None): |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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79 if missing: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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80 self.__missing = missing |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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81 if getsizeof: |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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82 self.__getsizeof = getsizeof |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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83 self.__size = dict() |
51ac1ffb4f38
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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84 self.__data = dict() |
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85 self.__currsize = 0 |
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86 self.__maxsize = maxsize |
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87 |
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88 def __repr__(self): |
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89 return '%s(%r, maxsize=%r, currsize=%r)' % ( |
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90 self.__class__.__name__, |
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91 list(self.__data.items()), |
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92 self.__maxsize, |
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93 self.__currsize, |
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94 ) |
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95 |
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96 def __getitem__(self, key): |
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97 try: |
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98 return self.__data[key] |
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99 except KeyError: |
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100 return self.__missing__(key) |
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101 |
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102 def __setitem__(self, key, value): |
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103 maxsize = self.__maxsize |
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104 size = self.getsizeof(value) |
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105 if size > maxsize: |
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106 raise ValueError('value too large') |
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107 if key not in self.__data or self.__size[key] < size: |
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108 while self.__currsize + size > maxsize: |
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109 self.popitem() |
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110 if key in self.__data: |
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111 diffsize = size - self.__size[key] |
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112 else: |
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113 diffsize = size |
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114 self.__data[key] = value |
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115 self.__size[key] = size |
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116 self.__currsize += diffsize |
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117 |
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118 def __delitem__(self, key): |
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119 size = self.__size.pop(key) |
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120 del self.__data[key] |
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121 self.__currsize -= size |
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122 |
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123 def __contains__(self, key): |
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124 return key in self.__data |
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125 |
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126 def __missing__(self, key): |
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127 value = self.__missing(key) |
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128 try: |
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129 self.__setitem__(key, value) |
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130 except ValueError: |
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131 pass # value too large |
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132 return value |
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133 |
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134 def __iter__(self): |
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135 return iter(self.__data) |
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136 |
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137 def __len__(self): |
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138 return len(self.__data) |
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139 |
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140 @staticmethod |
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141 def __getsizeof(value): |
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142 return 1 |
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143 |
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144 @staticmethod |
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145 def __missing(key): |
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146 raise KeyError(key) |
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147 |
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148 @property |
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149 def maxsize(self): |
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150 """The maximum size of the cache.""" |
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151 return self.__maxsize |
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152 |
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153 @property |
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154 def currsize(self): |
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155 """The current size of the cache.""" |
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156 return self.__currsize |
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157 |
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158 def getsizeof(self, value): |
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159 """Return the size of a cache element's value.""" |
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160 return self.__getsizeof(value) |
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161 |
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162 |
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163 class _Link(object): |
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164 |
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165 __slots__ = ('key', 'expire', 'next', 'prev') |
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166 |
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167 def __init__(self, key=None, expire=None): |
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168 self.key = key |
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169 self.expire = expire |
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170 |
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171 def __reduce__(self): |
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172 return _Link, (self.key, self.expire) |
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173 |
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174 def unlink(self): |
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175 next = self.next |
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176 prev = self.prev |
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177 prev.next = next |
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178 next.prev = prev |
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179 |
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180 |
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181 class _Timer(object): |
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182 |
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183 def __init__(self, timer): |
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184 self.__timer = timer |
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185 self.__nesting = 0 |
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186 |
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187 def __call__(self): |
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188 if self.__nesting == 0: |
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189 return self.__timer() |
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190 else: |
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191 return self.__time |
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192 |
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193 def __enter__(self): |
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194 if self.__nesting == 0: |
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195 self.__time = time = self.__timer() |
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196 else: |
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197 time = self.__time |
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198 self.__nesting += 1 |
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199 return time |
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200 |
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201 def __exit__(self, *exc): |
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202 self.__nesting -= 1 |
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203 |
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204 def __reduce__(self): |
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205 return _Timer, (self.__timer,) |
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206 |
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207 def __getattr__(self, name): |
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208 return getattr(self.__timer, name) |
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209 |
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210 |
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211 class TTLCache(Cache): |
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212 """LRU Cache implementation with per-item time-to-live (TTL) value.""" |
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213 |
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214 def __init__(self, maxsize, ttl, timer=time.time, missing=None, |
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215 getsizeof=None): |
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216 Cache.__init__(self, maxsize, missing, getsizeof) |
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217 self.__root = root = _Link() |
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218 root.prev = root.next = root |
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219 self.__links = collections.OrderedDict() |
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220 self.__timer = _Timer(timer) |
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221 self.__ttl = ttl |
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222 |
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223 def __contains__(self, key): |
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224 try: |
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225 link = self.__links[key] # no reordering |
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226 except KeyError: |
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227 return False |
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228 else: |
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229 return not (link.expire < self.__timer()) |
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230 |
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231 def __getitem__(self, key, cache_getitem=Cache.__getitem__): |
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232 try: |
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233 link = self.__getlink(key) |
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234 except KeyError: |
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235 expired = False |
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236 else: |
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237 expired = link.expire < self.__timer() |
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238 if expired: |
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239 return self.__missing__(key) |
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240 else: |
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241 return cache_getitem(self, key) |
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242 |
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243 def __setitem__(self, key, value, cache_setitem=Cache.__setitem__): |
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244 with self.__timer as time: |
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245 self.expire(time) |
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246 cache_setitem(self, key, value) |
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247 try: |
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248 link = self.__getlink(key) |
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249 except KeyError: |
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250 self.__links[key] = link = _Link(key) |
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251 else: |
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252 link.unlink() |
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253 link.expire = time + self.__ttl |
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254 link.next = root = self.__root |
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255 link.prev = prev = root.prev |
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256 prev.next = root.prev = link |
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257 |
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258 def __delitem__(self, key, cache_delitem=Cache.__delitem__): |
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259 cache_delitem(self, key) |
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260 link = self.__links.pop(key) |
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261 link.unlink() |
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262 if link.expire < self.__timer(): |
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263 raise KeyError(key) |
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264 |
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265 def __iter__(self): |
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266 root = self.__root |
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267 curr = root.next |
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268 while curr is not root: |
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269 # "freeze" time for iterator access |
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270 with self.__timer as time: |
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271 if not (curr.expire < time): |
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272 yield curr.key |
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273 curr = curr.next |
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274 |
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275 def __len__(self): |
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276 root = self.__root |
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277 curr = root.next |
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278 time = self.__timer() |
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279 count = len(self.__links) |
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280 while curr is not root and curr.expire < time: |
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281 count -= 1 |
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282 curr = curr.next |
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283 return count |
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284 |
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285 def __setstate__(self, state): |
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286 self.__dict__.update(state) |
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287 root = self.__root |
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288 root.prev = root.next = root |
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289 for link in sorted(self.__links.values(), key=lambda obj: obj.expire): |
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290 link.next = root |
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291 link.prev = prev = root.prev |
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292 prev.next = root.prev = link |
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293 self.expire(self.__timer()) |
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294 |
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295 def __repr__(self, cache_repr=Cache.__repr__): |
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296 with self.__timer as time: |
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297 self.expire(time) |
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298 return cache_repr(self) |
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299 |
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300 @property |
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301 def currsize(self): |
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302 with self.__timer as time: |
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303 self.expire(time) |
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304 return super(TTLCache, self).currsize |
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305 |
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306 @property |
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307 def timer(self): |
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308 """The timer function used by the cache.""" |
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309 return self.__timer |
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310 |
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311 @property |
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312 def ttl(self): |
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313 """The time-to-live value of the cache's items.""" |
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314 return self.__ttl |
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315 |
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316 def expire(self, time=None): |
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317 """Remove expired items from the cache.""" |
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318 if time is None: |
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319 time = self.__timer() |
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320 root = self.__root |
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321 curr = root.next |
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322 links = self.__links |
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323 cache_delitem = Cache.__delitem__ |
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324 while curr is not root and curr.expire < time: |
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325 cache_delitem(self, curr.key) |
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326 del links[curr.key] |
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327 next = curr.next |
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328 curr.unlink() |
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329 curr = next |
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330 |
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331 def clear(self): |
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332 with self.__timer as time: |
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333 self.expire(time) |
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334 Cache.clear(self) |
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335 |
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336 def get(self, *args, **kwargs): |
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337 with self.__timer: |
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338 return Cache.get(self, *args, **kwargs) |
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339 |
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340 def pop(self, *args, **kwargs): |
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341 with self.__timer: |
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342 return Cache.pop(self, *args, **kwargs) |
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343 |
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344 def setdefault(self, *args, **kwargs): |
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345 with self.__timer: |
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346 return Cache.setdefault(self, *args, **kwargs) |
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347 |
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348 def popitem(self): |
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349 """Remove and return the `(key, value)` pair least recently used that |
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350 has not already expired. |
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351 |
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352 """ |
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353 with self.__timer as time: |
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354 self.expire(time) |
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355 try: |
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356 key = next(iter(self.__links)) |
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357 except StopIteration: |
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358 raise KeyError('%s is empty' % self.__class__.__name__) |
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359 else: |
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360 return (key, self.pop(key)) |
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361 |
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362 if hasattr(collections.OrderedDict, 'move_to_end'): |
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363 def __getlink(self, key): |
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364 value = self.__links[key] |
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365 self.__links.move_to_end(key) |
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366 return value |
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367 else: |
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368 def __getlink(self, key): |
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369 value = self.__links.pop(key) |
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370 self.__links[key] = value |
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371 return value |
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372 |
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373 |
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374 ############################################# |
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375 # END IMPORT OF CACHING LIBRARY # |
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376 ############################################# |
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377 |
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378 cache = TTLCache( |
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379 100, # Up to 100 items |
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380 1 * 60 # 5 minute cache life |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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381 ) |
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382 |
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383 |
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384 def _get_instance(): |
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385 return chado.ChadoInstance( |
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386 os.environ['GALAXY_CHADO_DBHOST'], |
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387 os.environ['GALAXY_CHADO_DBNAME'], |
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388 os.environ['GALAXY_CHADO_DBUSER'], |
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389 os.environ['GALAXY_CHADO_DBPASS'], |
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390 os.environ['GALAXY_CHADO_DBSCHEMA'], |
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391 os.environ['GALAXY_CHADO_DBPORT'], |
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392 no_reflect=True |
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393 ) |
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394 |
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395 |
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396 def list_organisms(*args, **kwargs): |
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397 |
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398 ci = _get_instance() |
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399 |
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400 # Key for cached data |
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401 cacheKey = 'orgs' |
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402 # We don't want to trust "if key in cache" because between asking and fetch |
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403 # it might through key error. |
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404 if cacheKey not in cache: |
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405 # However if it ISN'T there, we know we're safe to fetch + put in |
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406 # there. |
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407 data = _list_organisms(ci, *args, **kwargs) |
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408 cache[cacheKey] = data |
7
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409 ci.session.close() |
0
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410 return data |
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411 try: |
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412 # The cache key may or may not be in the cache at this point, it |
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413 # /likely/ is. However we take no chances that it wasn't evicted between |
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414 # when we checked above and now, so we reference the object from the |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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415 # cache in preparation to return. |
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416 data = cache[cacheKey] |
7
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417 ci.session.close() |
0
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418 return data |
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419 except KeyError: |
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420 # If access fails due to eviction, we will fail over and can ensure that |
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421 # data is inserted. |
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422 data = _list_organisms(ci, *args, **kwargs) |
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423 cache[cacheKey] = data |
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424 ci.session.close() |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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425 return data |
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426 |
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427 |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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428 def _list_organisms(ci, *args, **kwargs): |
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429 # Fetch the orgs. |
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430 orgs_data = [] |
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431 for org in ci.organism.get_organisms(): |
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432 clean_name = '%s %s' % (org['genus'], org['species']) |
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433 if 'infraspecific_name' in org and org['infraspecific_name']: |
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434 clean_name += ' (%s)' % (org['infraspecific_name']) |
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435 orgs_data.append((clean_name, str(org['organism_id']), False)) |
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436 return orgs_data |
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437 |
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438 |
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439 def list_analyses(*args, **kwargs): |
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440 |
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441 ci = _get_instance() |
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442 |
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443 # Key for cached data |
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444 cacheKey = 'analyses' |
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445 # We don't want to trust "if key in cache" because between asking and fetch |
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446 # it might through key error. |
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447 if cacheKey not in cache: |
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448 # However if it ISN'T there, we know we're safe to fetch + put in |
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449 # there.<?xml version="1.0"?> |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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450 |
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451 data = _list_analyses(ci, *args, **kwargs) |
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452 cache[cacheKey] = data |
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453 ci.session.close() |
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454 return data |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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455 try: |
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456 # The cache key may or may not be in the cache at this point, it |
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457 # /likely/ is. However we take no chances that it wasn't evicted between |
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458 # when we checked above and now, so we reference the object from the |
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459 # cache in preparation to return. |
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460 data = cache[cacheKey] |
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461 ci.session.close() |
0
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462 return data |
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463 except KeyError: |
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464 # If access fails due to eviction, we will fail over and can ensure that |
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465 # data is inserted. |
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466 data = _list_analyses(ci, *args, **kwargs) |
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467 cache[cacheKey] = data |
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468 ci.session.close() |
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469 return data |
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470 |
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471 |
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472 def _list_analyses(ci, *args, **kwargs): |
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473 ans_data = [] |
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474 for an in ci.analysis.get_analyses(): |
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475 ans_data.append((an['name'], str(an['analysis_id']), False)) |
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476 return ans_data |