Mercurial > repos > gga > tripal_analysis_get_analyses
annotate tripal.py @ 0:0d3e2ed34956 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author | gga |
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date | Mon, 11 Sep 2017 05:49:54 -0400 (2017-09-11) |
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children | 92ffaac1d5df |
rev | line source |
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0
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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1 import collections |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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2 import os |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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3 import time |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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4 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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5 from abc import abstractmethod |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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6 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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7 import tripal |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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8 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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9 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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10 ############################################# |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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11 # BEGIN IMPORT OF CACHING LIBRARY # |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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12 ############################################# |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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13 # This code is licensed under the MIT # |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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14 # License and is a copy of code publicly # |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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15 # available in rev. # |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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16 # e27332bc82f4e327aedaec17c9b656ae719322ed # |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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17 # of https://github.com/tkem/cachetools/ # |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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18 ############################################# |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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19 class DefaultMapping(collections.MutableMapping): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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20 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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21 __slots__ = () |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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22 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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23 @abstractmethod |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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24 def __contains__(self, key): # pragma: nocover |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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25 return False |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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26 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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27 @abstractmethod |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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28 def __getitem__(self, key): # pragma: nocover |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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29 if hasattr(self.__class__, '__missing__'): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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30 return self.__class__.__missing__(self, key) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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31 else: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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32 raise KeyError(key) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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33 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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34 def get(self, key, default=None): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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35 if key in self: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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36 return self[key] |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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37 else: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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38 return default |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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39 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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40 __marker = object() |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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41 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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42 def pop(self, key, default=__marker): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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43 if key in self: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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44 value = self[key] |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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45 del self[key] |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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46 elif default is self.__marker: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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47 raise KeyError(key) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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48 else: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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49 value = default |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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50 return value |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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51 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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52 def setdefault(self, key, default=None): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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53 if key in self: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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54 value = self[key] |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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55 else: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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56 self[key] = value = default |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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57 return value |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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58 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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59 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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60 DefaultMapping.register(dict) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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61 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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62 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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63 class _DefaultSize(object): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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64 def __getitem__(self, _): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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65 return 1 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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66 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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67 def __setitem__(self, _, value): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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68 assert value == 1 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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69 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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70 def pop(self, _): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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71 return 1 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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72 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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73 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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74 class Cache(DefaultMapping): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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75 """Mutable mapping to serve as a simple cache or cache base class.""" |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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76 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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77 __size = _DefaultSize() |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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78 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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79 def __init__(self, maxsize, missing=None, getsizeof=None): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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80 if missing: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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81 self.__missing = missing |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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82 if getsizeof: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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83 self.__getsizeof = getsizeof |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
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84 self.__size = dict() |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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85 self.__data = dict() |
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86 self.__currsize = 0 |
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87 self.__maxsize = maxsize |
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88 |
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89 def __repr__(self): |
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90 return '%s(%r, maxsize=%r, currsize=%r)' % ( |
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91 self.__class__.__name__, |
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92 list(self.__data.items()), |
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93 self.__maxsize, |
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94 self.__currsize, |
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95 ) |
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96 |
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97 def __getitem__(self, key): |
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98 try: |
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99 return self.__data[key] |
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100 except KeyError: |
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101 return self.__missing__(key) |
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102 |
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103 def __setitem__(self, key, value): |
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104 maxsize = self.__maxsize |
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105 size = self.getsizeof(value) |
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106 if size > maxsize: |
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107 raise ValueError('value too large') |
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108 if key not in self.__data or self.__size[key] < size: |
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109 while self.__currsize + size > maxsize: |
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110 self.popitem() |
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111 if key in self.__data: |
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112 diffsize = size - self.__size[key] |
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113 else: |
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114 diffsize = size |
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115 self.__data[key] = value |
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116 self.__size[key] = size |
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117 self.__currsize += diffsize |
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118 |
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119 def __delitem__(self, key): |
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120 size = self.__size.pop(key) |
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121 del self.__data[key] |
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122 self.__currsize -= size |
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123 |
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124 def __contains__(self, key): |
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125 return key in self.__data |
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126 |
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127 def __missing__(self, key): |
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128 value = self.__missing(key) |
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129 try: |
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130 self.__setitem__(key, value) |
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131 except ValueError: |
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132 pass # value too large |
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133 return value |
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134 |
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135 def __iter__(self): |
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136 return iter(self.__data) |
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137 |
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138 def __len__(self): |
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139 return len(self.__data) |
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140 |
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141 @staticmethod |
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142 def __getsizeof(value): |
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143 return 1 |
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144 |
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145 @staticmethod |
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146 def __missing(key): |
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147 raise KeyError(key) |
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148 |
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149 @property |
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150 def maxsize(self): |
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151 """The maximum size of the cache.""" |
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152 return self.__maxsize |
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153 |
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154 @property |
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155 def currsize(self): |
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156 """The current size of the cache.""" |
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157 return self.__currsize |
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158 |
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159 def getsizeof(self, value): |
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160 """Return the size of a cache element's value.""" |
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161 return self.__getsizeof(value) |
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162 |
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163 |
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164 class _Link(object): |
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165 |
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166 __slots__ = ('key', 'expire', 'next', 'prev') |
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167 |
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168 def __init__(self, key=None, expire=None): |
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169 self.key = key |
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170 self.expire = expire |
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171 |
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172 def __reduce__(self): |
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173 return _Link, (self.key, self.expire) |
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174 |
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175 def unlink(self): |
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176 next = self.next |
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177 prev = self.prev |
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178 prev.next = next |
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179 next.prev = prev |
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180 |
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181 |
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182 class _Timer(object): |
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183 |
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184 def __init__(self, timer): |
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185 self.__timer = timer |
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186 self.__nesting = 0 |
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187 |
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188 def __call__(self): |
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189 if self.__nesting == 0: |
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190 return self.__timer() |
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191 else: |
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192 return self.__time |
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193 |
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194 def __enter__(self): |
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195 if self.__nesting == 0: |
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196 self.__time = time = self.__timer() |
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197 else: |
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198 time = self.__time |
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199 self.__nesting += 1 |
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200 return time |
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201 |
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202 def __exit__(self, *exc): |
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203 self.__nesting -= 1 |
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204 |
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205 def __reduce__(self): |
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206 return _Timer, (self.__timer,) |
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207 |
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208 def __getattr__(self, name): |
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209 return getattr(self.__timer, name) |
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210 |
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211 |
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212 class TTLCache(Cache): |
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213 """LRU Cache implementation with per-item time-to-live (TTL) value.""" |
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214 |
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215 def __init__(self, maxsize, ttl, timer=time.time, missing=None, |
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216 getsizeof=None): |
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217 Cache.__init__(self, maxsize, missing, getsizeof) |
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218 self.__root = root = _Link() |
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219 root.prev = root.next = root |
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220 self.__links = collections.OrderedDict() |
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221 self.__timer = _Timer(timer) |
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222 self.__ttl = ttl |
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223 |
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224 def __contains__(self, key): |
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225 try: |
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226 link = self.__links[key] # no reordering |
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227 except KeyError: |
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228 return False |
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229 else: |
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230 return not (link.expire < self.__timer()) |
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231 |
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232 def __getitem__(self, key, cache_getitem=Cache.__getitem__): |
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233 try: |
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234 link = self.__getlink(key) |
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235 except KeyError: |
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236 expired = False |
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237 else: |
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238 expired = link.expire < self.__timer() |
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239 if expired: |
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240 return self.__missing__(key) |
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241 else: |
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242 return cache_getitem(self, key) |
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243 |
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244 def __setitem__(self, key, value, cache_setitem=Cache.__setitem__): |
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245 with self.__timer as time: |
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246 self.expire(time) |
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247 cache_setitem(self, key, value) |
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248 try: |
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249 link = self.__getlink(key) |
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250 except KeyError: |
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251 self.__links[key] = link = _Link(key) |
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252 else: |
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253 link.unlink() |
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254 link.expire = time + self.__ttl |
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255 link.next = root = self.__root |
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256 link.prev = prev = root.prev |
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257 prev.next = root.prev = link |
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258 |
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259 def __delitem__(self, key, cache_delitem=Cache.__delitem__): |
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260 cache_delitem(self, key) |
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261 link = self.__links.pop(key) |
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262 link.unlink() |
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263 if link.expire < self.__timer(): |
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264 raise KeyError(key) |
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265 |
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266 def __iter__(self): |
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267 root = self.__root |
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268 curr = root.next |
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269 while curr is not root: |
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270 # "freeze" time for iterator access |
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271 with self.__timer as time: |
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272 if not (curr.expire < time): |
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273 yield curr.key |
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274 curr = curr.next |
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275 |
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276 def __len__(self): |
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277 root = self.__root |
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278 curr = root.next |
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279 time = self.__timer() |
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280 count = len(self.__links) |
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281 while curr is not root and curr.expire < time: |
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282 count -= 1 |
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283 curr = curr.next |
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284 return count |
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285 |
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286 def __setstate__(self, state): |
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287 self.__dict__.update(state) |
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288 root = self.__root |
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289 root.prev = root.next = root |
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290 for link in sorted(self.__links.values(), key=lambda obj: obj.expire): |
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291 link.next = root |
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292 link.prev = prev = root.prev |
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293 prev.next = root.prev = link |
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294 self.expire(self.__timer()) |
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295 |
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296 def __repr__(self, cache_repr=Cache.__repr__): |
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297 with self.__timer as time: |
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298 self.expire(time) |
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299 return cache_repr(self) |
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300 |
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301 @property |
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302 def currsize(self): |
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303 with self.__timer as time: |
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304 self.expire(time) |
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305 return super(TTLCache, self).currsize |
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306 |
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307 @property |
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308 def timer(self): |
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309 """The timer function used by the cache.""" |
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310 return self.__timer |
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311 |
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312 @property |
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313 def ttl(self): |
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314 """The time-to-live value of the cache's items.""" |
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315 return self.__ttl |
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316 |
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317 def expire(self, time=None): |
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318 """Remove expired items from the cache.""" |
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319 if time is None: |
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320 time = self.__timer() |
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321 root = self.__root |
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322 curr = root.next |
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323 links = self.__links |
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324 cache_delitem = Cache.__delitem__ |
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325 while curr is not root and curr.expire < time: |
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326 cache_delitem(self, curr.key) |
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327 del links[curr.key] |
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328 next = curr.next |
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329 curr.unlink() |
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330 curr = next |
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331 |
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332 def clear(self): |
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333 with self.__timer as time: |
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334 self.expire(time) |
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335 Cache.clear(self) |
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336 |
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337 def get(self, *args, **kwargs): |
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338 with self.__timer: |
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339 return Cache.get(self, *args, **kwargs) |
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340 |
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341 def pop(self, *args, **kwargs): |
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342 with self.__timer: |
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343 return Cache.pop(self, *args, **kwargs) |
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344 |
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345 def setdefault(self, *args, **kwargs): |
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346 with self.__timer: |
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347 return Cache.setdefault(self, *args, **kwargs) |
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348 |
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349 def popitem(self): |
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350 """Remove and return the `(key, value)` pair least recently used that |
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351 has not already expired. |
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352 |
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353 """ |
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354 with self.__timer as time: |
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355 self.expire(time) |
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356 try: |
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357 key = next(iter(self.__links)) |
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358 except StopIteration: |
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359 raise KeyError('%s is empty' % self.__class__.__name__) |
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360 else: |
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361 return (key, self.pop(key)) |
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362 |
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363 if hasattr(collections.OrderedDict, 'move_to_end'): |
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364 def __getlink(self, key): |
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365 value = self.__links[key] |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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366 self.__links.move_to_end(key) |
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367 return value |
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368 else: |
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369 def __getlink(self, key): |
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370 value = self.__links.pop(key) |
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371 self.__links[key] = value |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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372 return value |
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373 |
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374 |
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375 ############################################# |
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376 # END IMPORT OF CACHING LIBRARY # |
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377 ############################################# |
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378 |
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379 cache = TTLCache( |
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380 100, # Up to 100 items |
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381 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/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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382 ) |
0d3e2ed34956
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383 |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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384 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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385 def _get_instance(): |
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386 return tripal.TripalInstance( |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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387 os.environ['GALAXY_TRIPAL_URL'], |
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388 os.environ['GALAXY_TRIPAL_USER'], |
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389 os.environ['GALAXY_TRIPAL_PASSWORD'] |
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390 ) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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391 |
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392 |
0d3e2ed34956
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393 def list_organisms(*args, **kwargs): |
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394 |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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395 ti = _get_instance() |
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396 |
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397 # Key for cached data |
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398 cacheKey = 'orgs' |
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399 # We don't want to trust "if key in cache" because between asking and fetch |
0d3e2ed34956
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400 # it might through key error. |
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401 if cacheKey not in cache: |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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402 # However if it ISN'T there, we know we're safe to fetch + put in |
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403 # there. |
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404 data = _list_organisms(ti, *args, **kwargs) |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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405 cache[cacheKey] = data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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406 return data |
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407 try: |
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408 # The cache key may or may not be in the cache at this point, it |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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409 # /likely/ is. However we take no chances that it wasn't evicted between |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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410 # when we checked above and now, so we reference the object from the |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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411 # cache in preparation to return. |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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412 data = cache[cacheKey] |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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413 return data |
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414 except KeyError: |
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415 # If access fails due to eviction, we will fail over and can ensure that |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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416 # data is inserted. |
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417 data = _list_organisms(ti, *args, **kwargs) |
0d3e2ed34956
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418 cache[cacheKey] = data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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419 return data |
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420 |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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421 |
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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422 def _list_organisms(ti, *args, **kwargs): |
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423 # Fetch the orgs. |
0d3e2ed34956
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424 orgs_data = [] |
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425 for org in ti.organism.get_organisms(): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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426 clean_name = '%s %s' % (org['genus'], org['species']) |
0d3e2ed34956
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427 if org['infraspecific_name']: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff
changeset
|
428 clean_name += ' (%s)' % (org['infraspecific_name']) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
429 orgs_data.append((clean_name, org['organism_id'], False)) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
430 return orgs_data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
431 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
432 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
433 def list_analyses(*args, **kwargs): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
434 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
435 ti = _get_instance() |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
436 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
437 # Key for cached data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
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438 cacheKey = 'analyses' |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
439 # We don't want to trust "if key in cache" because between asking and fetch |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
440 # it might through key error. |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
441 if cacheKey not in cache: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
442 # However if it ISN'T there, we know we're safe to fetch + put in |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
443 # there.<?xml version="1.0"?> |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
444 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
445 data = _list_analyses(ti, *args, **kwargs) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
446 cache[cacheKey] = data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
447 return data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
448 try: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
449 # The cache key may or may not be in the cache at this point, it |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
450 # /likely/ is. However we take no chances that it wasn't evicted between |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
451 # when we checked above and now, so we reference the object from the |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
452 # cache in preparation to return. |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
453 data = cache[cacheKey] |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
454 return data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
455 except KeyError: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
456 # If access fails due to eviction, we will fail over and can ensure that |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
457 # data is inserted. |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
458 data = _list_analyses(ti, *args, **kwargs) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
459 cache[cacheKey] = data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
460 return data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
461 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
462 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
463 def _list_analyses(ti, *args, **kwargs): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
464 ans_data = [] |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
465 for an in ti.analysis.get_analyses(): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
466 ans_data.append((an['name'], an['analysis_id'], False)) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
467 return ans_data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
468 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
469 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
470 def list_blastdbs(*args, **kwargs): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
471 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
472 ti = _get_instance() |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
473 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
474 # Key for cached data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
475 cacheKey = 'blastdbs' |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
476 # We don't want to trust "if key in cache" because between asking and fetch |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
477 # it might through key error. |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
478 if cacheKey not in cache: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
479 # However if it ISN'T there, we know we're safe to fetch + put in |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
480 # there. |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
481 data = _list_blastdbs(ti, *args, **kwargs) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
482 cache[cacheKey] = data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
483 return data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
484 try: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
485 # The cache key may or may not be in the cache at this point, it |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
486 # /likely/ is. However we take no chances that it wasn't evicted between |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
487 # when we checked above and now, so we reference the object from the |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
488 # cache in preparation to return. |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
489 data = cache[cacheKey] |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
490 return data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
491 except KeyError: |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
492 # If access fails due to eviction, we will fail over and can ensure that |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
493 # data is inserted. |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
494 data = _list_blastdbs(ti, *args, **kwargs) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
495 cache[cacheKey] = data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
496 return data |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
497 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
498 |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
499 def _list_blastdbs(ti, *args, **kwargs): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
500 dbs_data = [] |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
501 for db in ti.db.get_dbs(): |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
502 dbs_data.append((db['name'], db['db_id'], False)) |
0d3e2ed34956
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff
changeset
|
503 return dbs_data |