Mercurial > repos > gga > chado_load_interpro

annotate chado.py @ 0:0805e7b3254d draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
author gga
date Wed, 21 Aug 2019 05:07:40 -0400
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0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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1 import collections
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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2 import os
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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3 import time
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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4 from abc import abstractmethod
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5
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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6 import chado
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7
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8
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9 #############################################
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10 # BEGIN IMPORT OF CACHING LIBRARY #
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11 #############################################
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12 # This code is licensed under the MIT #
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13 # License and is a copy of code publicly #
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14 # available in rev. #
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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15 # e27332bc82f4e327aedaec17c9b656ae719322ed #
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16 # of https://github.com/tkem/cachetools/ #
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17 #############################################
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18 class DefaultMapping(collections.MutableMapping):
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19
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20 __slots__ = ()
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21
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22 @abstractmethod
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23 def __contains__(self, key): # pragma: nocover
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24 return False
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26 @abstractmethod
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27 def __getitem__(self, key): # pragma: nocover
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28 if hasattr(self.__class__, '__missing__'):
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29 return self.__class__.__missing__(self, key)
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30 else:
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31 raise KeyError(key)
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32
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33 def get(self, key, default=None):
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34 if key in self:
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35 return self[key]
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36 else:
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37 return default
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38
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39 __marker = object()
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41 def pop(self, key, default=__marker):
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42 if key in self:
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43 value = self[key]
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44 del self[key]
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45 elif default is self.__marker:
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46 raise KeyError(key)
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47 else:
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48 value = default
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49 return value
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50
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51 def setdefault(self, key, default=None):
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52 if key in self:
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53 value = self[key]
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54 else:
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55 self[key] = value = default
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56 return value
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57
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58
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59 DefaultMapping.register(dict)
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60
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61
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62 class _DefaultSize(object):
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63 def __getitem__(self, _):
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64 return 1
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65
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66 def __setitem__(self, _, value):
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67 assert value == 1
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68
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69 def pop(self, _):
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70 return 1
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71
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72
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73 class Cache(DefaultMapping):
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74 """Mutable mapping to serve as a simple cache or cache base class."""
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75
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76 __size = _DefaultSize()
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77
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78 def __init__(self, maxsize, missing=None, getsizeof=None):
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79 if missing:
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80 self.__missing = missing
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81 if getsizeof:
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82 self.__getsizeof = getsizeof
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83 self.__size = dict()
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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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gga
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diff changeset
90 self.__class__.__name__,
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
91 list(self.__data.items()),
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
92 self.__maxsize,
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
93 self.__currsize,
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
94 )
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
95
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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96 def __getitem__(self, key):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
97 try:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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98 return self.__data[key]
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
99 except KeyError:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
100 return self.__missing__(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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101
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
102 def __setitem__(self, key, value):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
103 maxsize = self.__maxsize
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
104 size = self.getsizeof(value)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
105 if size > maxsize:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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106 raise ValueError('value too large')
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
107 if key not in self.__data or self.__size[key] < size:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
108 while self.__currsize + size > maxsize:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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109 self.popitem()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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110 if key in self.__data:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
111 diffsize = size - self.__size[key]
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
112 else:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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113 diffsize = size
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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114 self.__data[key] = value
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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115 self.__size[key] = size
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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116 self.__currsize += diffsize
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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117
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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118 def __delitem__(self, key):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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119 size = self.__size.pop(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
120 del self.__data[key]
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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121 self.__currsize -= size
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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122
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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123 def __contains__(self, key):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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124 return key in self.__data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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125
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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126 def __missing__(self, key):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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127 value = self.__missing(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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128 try:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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129 self.__setitem__(key, value)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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130 except ValueError:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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131 pass # value too large
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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132 return value
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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133
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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134 def __iter__(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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135 return iter(self.__data)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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136
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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137 def __len__(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
138 return len(self.__data)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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139
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
140 @staticmethod
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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141 def __getsizeof(value):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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142 return 1
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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143
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
144 @staticmethod
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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145 def __missing(key):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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146 raise KeyError(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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147
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
148 @property
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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149 def maxsize(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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150 """The maximum size of the cache."""
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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151 return self.__maxsize
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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152
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
153 @property
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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154 def currsize(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
155 """The current size of the cache."""
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
156 return self.__currsize
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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157
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
158 def getsizeof(self, value):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
159 """Return the size of a cache element's value."""
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
160 return self.__getsizeof(value)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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161
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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162
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
163 class _Link(object):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
164
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
165 __slots__ = ('key', 'expire', 'next', 'prev')
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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166
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
167 def __init__(self, key=None, expire=None):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
168 self.key = key
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
169 self.expire = expire
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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170
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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171 def __reduce__(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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172 return _Link, (self.key, self.expire)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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173
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
174 def unlink(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
175 next = self.next
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
176 prev = self.prev
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
177 prev.next = next
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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178 next.prev = prev
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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179
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
180
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
181 class _Timer(object):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
182
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
183 def __init__(self, timer):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
184 self.__timer = timer
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
185 self.__nesting = 0
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
186
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
187 def __call__(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
188 if self.__nesting == 0:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
189 return self.__timer()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
190 else:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
191 return self.__time
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
192
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
193 def __enter__(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
194 if self.__nesting == 0:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
195 self.__time = time = self.__timer()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
196 else:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
197 time = self.__time
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
198 self.__nesting += 1
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
199 return time
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
200
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
201 def __exit__(self, *exc):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
202 self.__nesting -= 1
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
203
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
204 def __reduce__(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
205 return _Timer, (self.__timer,)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
206
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
207 def __getattr__(self, name):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
208 return getattr(self.__timer, name)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
209
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
210
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
211 class TTLCache(Cache):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
212 """LRU Cache implementation with per-item time-to-live (TTL) value."""
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
213
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
214 def __init__(self, maxsize, ttl, timer=time.time, missing=None,
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
215 getsizeof=None):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
216 Cache.__init__(self, maxsize, missing, getsizeof)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
217 self.__root = root = _Link()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
218 root.prev = root.next = root
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
219 self.__links = collections.OrderedDict()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
220 self.__timer = _Timer(timer)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
221 self.__ttl = ttl
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
222
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
223 def __contains__(self, key):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
224 try:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
225 link = self.__links[key] # no reordering
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
226 except KeyError:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
227 return False
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
228 else:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
229 return not (link.expire < self.__timer())
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
230
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
231 def __getitem__(self, key, cache_getitem=Cache.__getitem__):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
232 try:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
233 link = self.__getlink(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
234 except KeyError:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
235 expired = False
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
236 else:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
237 expired = link.expire < self.__timer()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
238 if expired:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
239 return self.__missing__(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
240 else:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
241 return cache_getitem(self, key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
242
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
243 def __setitem__(self, key, value, cache_setitem=Cache.__setitem__):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
244 with self.__timer as time:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
245 self.expire(time)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
246 cache_setitem(self, key, value)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
247 try:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
248 link = self.__getlink(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
249 except KeyError:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
250 self.__links[key] = link = _Link(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
251 else:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
252 link.unlink()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
253 link.expire = time + self.__ttl
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
254 link.next = root = self.__root
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
255 link.prev = prev = root.prev
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
256 prev.next = root.prev = link
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
257
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
258 def __delitem__(self, key, cache_delitem=Cache.__delitem__):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
259 cache_delitem(self, key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
260 link = self.__links.pop(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
261 link.unlink()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
262 if link.expire < self.__timer():
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
263 raise KeyError(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
264
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
265 def __iter__(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
266 root = self.__root
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
267 curr = root.next
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
268 while curr is not root:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
269 # "freeze" time for iterator access
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
270 with self.__timer as time:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
271 if not (curr.expire < time):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
272 yield curr.key
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
273 curr = curr.next
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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274
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
275 def __len__(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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276 root = self.__root
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
277 curr = root.next
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
278 time = self.__timer()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
279 count = len(self.__links)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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280 while curr is not root and curr.expire < time:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
281 count -= 1
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
282 curr = curr.next
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
283 return count
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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284
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
285 def __setstate__(self, state):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
286 self.__dict__.update(state)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
287 root = self.__root
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
288 root.prev = root.next = root
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
289 for link in sorted(self.__links.values(), key=lambda obj: obj.expire):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
290 link.next = root
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
291 link.prev = prev = root.prev
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
292 prev.next = root.prev = link
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
293 self.expire(self.__timer())
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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294
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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295 def __repr__(self, cache_repr=Cache.__repr__):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
296 with self.__timer as time:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
297 self.expire(time)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
298 return cache_repr(self)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
299
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
300 @property
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
301 def currsize(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
302 with self.__timer as time:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
303 self.expire(time)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
304 return super(TTLCache, self).currsize
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
305
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
306 @property
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
307 def timer(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
308 """The timer function used by the cache."""
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
309 return self.__timer
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
310
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
311 @property
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
312 def ttl(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
313 """The time-to-live value of the cache's items."""
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
314 return self.__ttl
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
315
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
316 def expire(self, time=None):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
317 """Remove expired items from the cache."""
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
318 if time is None:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
319 time = self.__timer()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
320 root = self.__root
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
321 curr = root.next
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
322 links = self.__links
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
323 cache_delitem = Cache.__delitem__
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
324 while curr is not root and curr.expire < time:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
325 cache_delitem(self, curr.key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
326 del links[curr.key]
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
327 next = curr.next
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
328 curr.unlink()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
329 curr = next
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
330
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
331 def clear(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
332 with self.__timer as time:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
333 self.expire(time)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
334 Cache.clear(self)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
335
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
336 def get(self, *args, **kwargs):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
337 with self.__timer:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
338 return Cache.get(self, *args, **kwargs)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
339
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
340 def pop(self, *args, **kwargs):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
341 with self.__timer:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
342 return Cache.pop(self, *args, **kwargs)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
343
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
344 def setdefault(self, *args, **kwargs):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
345 with self.__timer:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
346 return Cache.setdefault(self, *args, **kwargs)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
347
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
348 def popitem(self):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
349 """Remove and return the `(key, value)` pair least recently used that
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
350 has not already expired.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
351
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
352 """
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
353 with self.__timer as time:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
354 self.expire(time)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
355 try:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
356 key = next(iter(self.__links))
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
357 except StopIteration:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
358 raise KeyError('%s is empty' % self.__class__.__name__)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
359 else:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
360 return (key, self.pop(key))
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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361
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
362 if hasattr(collections.OrderedDict, 'move_to_end'):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
363 def __getlink(self, key):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
364 value = self.__links[key]
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
365 self.__links.move_to_end(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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366 return value
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
367 else:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
368 def __getlink(self, key):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
369 value = self.__links.pop(key)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
370 self.__links[key] = value
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
371 return value
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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372
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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373
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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374 #############################################
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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375 # END IMPORT OF CACHING LIBRARY #
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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376 #############################################
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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377
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
378 cache = TTLCache(
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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379 100, # Up to 100 items
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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380 1 * 60 # 5 minute cache life
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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381 )
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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382
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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383
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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384 def _get_instance():
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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385 return chado.ChadoInstance(
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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386 os.environ['GALAXY_CHADO_DBHOST'],
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
387 os.environ['GALAXY_CHADO_DBNAME'],
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
388 os.environ['GALAXY_CHADO_DBUSER'],
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
389 os.environ['GALAXY_CHADO_DBPASS'],
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
390 os.environ['GALAXY_CHADO_DBSCHEMA'],
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
391 os.environ['GALAXY_CHADO_DBPORT'],
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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392 no_reflect=True,
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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393 pool_connections=False
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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394 )
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
395
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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396
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
397 def list_organisms(*args, **kwargs):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
398
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
399 ci = _get_instance()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
400
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
401 # Key for cached data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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402 cacheKey = 'orgs'
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
403 # We don't want to trust "if key in cache" because between asking and fetch
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
404 # it might through key error.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
405 if cacheKey not in cache:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
406 # However if it ISN'T there, we know we're safe to fetch + put in
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
407 # there.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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408 data = _list_organisms(ci, *args, **kwargs)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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409 cache[cacheKey] = data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
410 ci.session.close()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
411 return data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
412 try:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
413 # The cache key may or may not be in the cache at this point, it
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
414 # /likely/ is. However we take no chances that it wasn't evicted between
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
415 # when we checked above and now, so we reference the object from the
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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416 # cache in preparation to return.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
417 data = cache[cacheKey]
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
418 ci.session.close()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
419 return data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
420 except KeyError:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
421 # If access fails due to eviction, we will fail over and can ensure that
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
422 # data is inserted.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
423 data = _list_organisms(ci, *args, **kwargs)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
424 cache[cacheKey] = data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
425 ci.session.close()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
426 return data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
427
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
428
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
429 def _list_organisms(ci, *args, **kwargs):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
430 # Fetch the orgs.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
431 orgs_data = []
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
432 for org in ci.organism.get_organisms():
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
433 clean_name = '%s %s' % (org['genus'], org['species'])
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
434 if 'infraspecific_name' in org and org['infraspecific_name']:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
435 clean_name += ' (%s)' % (org['infraspecific_name'])
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
436 orgs_data.append((clean_name, str(org['organism_id']), False))
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
437 return orgs_data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
438
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
439
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
440 def list_analyses(*args, **kwargs):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
441
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
442 ci = _get_instance()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
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diff changeset
443
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
444 # Key for cached data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
445 cacheKey = 'analyses'
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
446 # We don't want to trust "if key in cache" because between asking and fetch
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
447 # it might through key error.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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diff changeset
448 if cacheKey not in cache:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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parents:
diff changeset
449 # However if it ISN'T there, we know we're safe to fetch + put in
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
450 # there.<?xml version="1.0"?>
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
451
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
452 data = _list_analyses(ci, *args, **kwargs)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
453 cache[cacheKey] = data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
454 ci.session.close()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
455 return data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
456 try:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
457 # The cache key may or may not be in the cache at this point, it
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
458 # /likely/ is. However we take no chances that it wasn't evicted between
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
459 # when we checked above and now, so we reference the object from the
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
460 # cache in preparation to return.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
461 data = cache[cacheKey]
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
462 ci.session.close()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
463 return data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
464 except KeyError:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
465 # If access fails due to eviction, we will fail over and can ensure that
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
466 # data is inserted.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
467 data = _list_analyses(ci, *args, **kwargs)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
468 cache[cacheKey] = data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
469 ci.session.close()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
470 return data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
471
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
472
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
473 def _list_analyses(ci, *args, **kwargs):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
474 ans_data = []
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
475 for an in ci.analysis.get_analyses():
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
476 ans_data.append((an['name'], str(an['analysis_id']), False))
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
477 return ans_data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
478
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
479
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
480 def list_dbs(*args, **kwargs):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
481
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
482 ci = _get_instance()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
483
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
484 # Key for cached data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
485 cacheKey = 'dbs'
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
486 # We don't want to trust "if key in cache" because between asking and fetch
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
487 # it might through key error.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
488 if cacheKey not in cache:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
489 # However if it ISN'T there, we know we're safe to fetch + put in
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
490 # there.<?xml version="1.0"?>
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
491
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
492 data = _list_dbs(ci, *args, **kwargs)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
493 cache[cacheKey] = data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
494 ci.session.close()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
495 return data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
496 try:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
497 # The cache key may or may not be in the cache at this point, it
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
498 # /likely/ is. However we take no chances that it wasn't evicted between
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
499 # when we checked above and now, so we reference the object from the
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
500 # cache in preparation to return.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
501 data = cache[cacheKey]
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
502 ci.session.close()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
503 return data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
504 except KeyError:
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
505 # If access fails due to eviction, we will fail over and can ensure that
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
506 # data is inserted.
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
507 data = _list_dbs(ci, *args, **kwargs)
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
508 cache[cacheKey] = data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
509 ci.session.close()
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
510 return data
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
511
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
512
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
513 def _list_dbs(ci, *args, **kwargs):
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
514 dbs_data = []
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
515 for db in ci.load._get_dbs():
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
516 dbs_data.append((db['name'], str(db['db_id']), False))
0805e7b3254d "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents:
diff changeset
517 return dbs_data