Mercurial > repos > gga > chado_phylogeny_gene_families

annotate chado.py @ 11:cb4cee85202a draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
author gga
date Mon, 08 Jul 2019 05:37:56 -0400
parents 9867cab3574b
children 1383275a8210
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e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
1 import collections
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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2 import os
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3 import time
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4 from abc import abstractmethod
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5
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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. #
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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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25
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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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40
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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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90 self.__class__.__name__,
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91 list(self.__data.items()),
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92 self.__maxsize,
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93 self.__currsize,
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94 )
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95
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96 def __getitem__(self, key):
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97 try:
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98 return self.__data[key]
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99 except KeyError:
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100 return self.__missing__(key)
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101
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102 def __setitem__(self, key, value):
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103 maxsize = self.__maxsize
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104 size = self.getsizeof(value)
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105 if size > maxsize:
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106 raise ValueError('value too large')
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107 if key not in self.__data or self.__size[key] < size:
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108 while self.__currsize + size > maxsize:
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109 self.popitem()
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110 if key in self.__data:
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111 diffsize = size - self.__size[key]
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112 else:
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113 diffsize = size
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114 self.__data[key] = value
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115 self.__size[key] = size
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116 self.__currsize += diffsize
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117
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118 def __delitem__(self, key):
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119 size = self.__size.pop(key)
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120 del self.__data[key]
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121 self.__currsize -= size
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122
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123 def __contains__(self, key):
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124 return key in self.__data
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125
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126 def __missing__(self, key):
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127 value = self.__missing(key)
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128 try:
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129 self.__setitem__(key, value)
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130 except ValueError:
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131 pass # value too large
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132 return value
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133
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134 def __iter__(self):
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135 return iter(self.__data)
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136
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137 def __len__(self):
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138 return len(self.__data)
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139
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140 @staticmethod
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141 def __getsizeof(value):
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142 return 1
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143
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144 @staticmethod
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145 def __missing(key):
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146 raise KeyError(key)
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147
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148 @property
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149 def maxsize(self):
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150 """The maximum size of the cache."""
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151 return self.__maxsize
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152
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153 @property
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154 def currsize(self):
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155 """The current size of the cache."""
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156 return self.__currsize
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157
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158 def getsizeof(self, value):
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159 """Return the size of a cache element's value."""
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160 return self.__getsizeof(value)
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161
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162
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163 class _Link(object):
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164
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165 __slots__ = ('key', 'expire', 'next', 'prev')
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166
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167 def __init__(self, key=None, expire=None):
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168 self.key = key
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169 self.expire = expire
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170
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171 def __reduce__(self):
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172 return _Link, (self.key, self.expire)
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173
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174 def unlink(self):
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175 next = self.next
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176 prev = self.prev
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177 prev.next = next
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178 next.prev = prev
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179
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180
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181 class _Timer(object):
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182
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183 def __init__(self, timer):
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184 self.__timer = timer
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185 self.__nesting = 0
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186
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187 def __call__(self):
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188 if self.__nesting == 0:
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189 return self.__timer()
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190 else:
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191 return self.__time
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192
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193 def __enter__(self):
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194 if self.__nesting == 0:
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195 self.__time = time = self.__timer()
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196 else:
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197 time = self.__time
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198 self.__nesting += 1
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199 return time
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200
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201 def __exit__(self, *exc):
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202 self.__nesting -= 1
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203
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204 def __reduce__(self):
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205 return _Timer, (self.__timer,)
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206
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207 def __getattr__(self, name):
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208 return getattr(self.__timer, name)
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209
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210
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211 class TTLCache(Cache):
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212 """LRU Cache implementation with per-item time-to-live (TTL) value."""
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213
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214 def __init__(self, maxsize, ttl, timer=time.time, missing=None,
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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215 getsizeof=None):
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216 Cache.__init__(self, maxsize, missing, getsizeof)
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217 self.__root = root = _Link()
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218 root.prev = root.next = root
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219 self.__links = collections.OrderedDict()
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220 self.__timer = _Timer(timer)
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221 self.__ttl = ttl
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222
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223 def __contains__(self, key):
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224 try:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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225 link = self.__links[key] # no reordering
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226 except KeyError:
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227 return False
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diff changeset
228 else:
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229 return not (link.expire < self.__timer())
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230
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231 def __getitem__(self, key, cache_getitem=Cache.__getitem__):
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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232 try:
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233 link = self.__getlink(key)
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234 except KeyError:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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235 expired = False
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
236 else:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
237 expired = link.expire < self.__timer()
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
238 if expired:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
diff changeset
239 return self.__missing__(key)
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
240 else:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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241 return cache_getitem(self, key)
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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242
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243 def __setitem__(self, key, value, cache_setitem=Cache.__setitem__):
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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244 with self.__timer as time:
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diff changeset
245 self.expire(time)
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diff changeset
246 cache_setitem(self, key, value)
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diff changeset
247 try:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
248 link = self.__getlink(key)
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diff changeset
249 except KeyError:
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250 self.__links[key] = link = _Link(key)
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diff changeset
251 else:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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252 link.unlink()
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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253 link.expire = time + self.__ttl
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
254 link.next = root = self.__root
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parents:
diff changeset
255 link.prev = prev = root.prev
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parents:
diff changeset
256 prev.next = root.prev = link
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257
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parents:
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258 def __delitem__(self, key, cache_delitem=Cache.__delitem__):
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
259 cache_delitem(self, key)
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diff changeset
260 link = self.__links.pop(key)
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parents:
diff changeset
261 link.unlink()
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
diff changeset
262 if link.expire < self.__timer():
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parents:
diff changeset
263 raise KeyError(key)
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diff changeset
264
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
diff changeset
265 def __iter__(self):
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
diff changeset
266 root = self.__root
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
diff changeset
267 curr = root.next
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
268 while curr is not root:
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parents:
diff changeset
269 # "freeze" time for iterator access
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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diff changeset
270 with self.__timer as time:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
diff changeset
271 if not (curr.expire < time):
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
diff changeset
272 yield curr.key
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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273 curr = curr.next
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274
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275 def __len__(self):
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276 root = self.__root
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277 curr = root.next
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278 time = self.__timer()
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279 count = len(self.__links)
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280 while curr is not root and curr.expire < time:
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281 count -= 1
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282 curr = curr.next
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283 return count
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284
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285 def __setstate__(self, state):
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286 self.__dict__.update(state)
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287 root = self.__root
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288 root.prev = root.next = root
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289 for link in sorted(self.__links.values(), key=lambda obj: obj.expire):
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290 link.next = root
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291 link.prev = prev = root.prev
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292 prev.next = root.prev = link
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293 self.expire(self.__timer())
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294
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295 def __repr__(self, cache_repr=Cache.__repr__):
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296 with self.__timer as time:
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297 self.expire(time)
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298 return cache_repr(self)
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299
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300 @property
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301 def currsize(self):
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302 with self.__timer as time:
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303 self.expire(time)
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304 return super(TTLCache, self).currsize
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305
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306 @property
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307 def timer(self):
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308 """The timer function used by the cache."""
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309 return self.__timer
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310
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311 @property
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312 def ttl(self):
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313 """The time-to-live value of the cache's items."""
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314 return self.__ttl
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315
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316 def expire(self, time=None):
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317 """Remove expired items from the cache."""
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318 if time is None:
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319 time = self.__timer()
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320 root = self.__root
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321 curr = root.next
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322 links = self.__links
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323 cache_delitem = Cache.__delitem__
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324 while curr is not root and curr.expire < time:
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325 cache_delitem(self, curr.key)
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326 del links[curr.key]
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327 next = curr.next
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328 curr.unlink()
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329 curr = next
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330
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331 def clear(self):
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332 with self.__timer as time:
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333 self.expire(time)
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334 Cache.clear(self)
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335
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336 def get(self, *args, **kwargs):
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337 with self.__timer:
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338 return Cache.get(self, *args, **kwargs)
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339
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340 def pop(self, *args, **kwargs):
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341 with self.__timer:
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342 return Cache.pop(self, *args, **kwargs)
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343
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344 def setdefault(self, *args, **kwargs):
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345 with self.__timer:
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346 return Cache.setdefault(self, *args, **kwargs)
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347
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348 def popitem(self):
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349 """Remove and return the `(key, value)` pair least recently used that
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350 has not already expired.
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351
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352 """
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353 with self.__timer as time:
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354 self.expire(time)
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355 try:
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356 key = next(iter(self.__links))
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357 except StopIteration:
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358 raise KeyError('%s is empty' % self.__class__.__name__)
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diff changeset
359 else:
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360 return (key, self.pop(key))
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361
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362 if hasattr(collections.OrderedDict, 'move_to_end'):
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363 def __getlink(self, key):
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364 value = self.__links[key]
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365 self.__links.move_to_end(key)
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366 return value
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367 else:
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368 def __getlink(self, key):
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369 value = self.__links.pop(key)
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370 self.__links[key] = value
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371 return value
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372
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373
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374 #############################################
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375 # END IMPORT OF CACHING LIBRARY #
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376 #############################################
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377
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378 cache = TTLCache(
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379 100, # Up to 100 items
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380 1 * 60 # 5 minute cache life
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381 )
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382
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383
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384 def _get_instance():
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385 return chado.ChadoInstance(
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386 os.environ['GALAXY_CHADO_DBHOST'],
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387 os.environ['GALAXY_CHADO_DBNAME'],
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388 os.environ['GALAXY_CHADO_DBUSER'],
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389 os.environ['GALAXY_CHADO_DBPASS'],
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390 os.environ['GALAXY_CHADO_DBSCHEMA'],
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391 os.environ['GALAXY_CHADO_DBPORT'],
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392 no_reflect=True
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393 )
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394
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395
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396 def list_organisms(*args, **kwargs):
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397
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398 ci = _get_instance()
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399
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400 # Key for cached data
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401 cacheKey = 'orgs'
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402 # We don't want to trust "if key in cache" because between asking and fetch
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403 # it might through key error.
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404 if cacheKey not in cache:
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405 # However if it ISN'T there, we know we're safe to fetch + put in
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406 # there.
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407 data = _list_organisms(ci, *args, **kwargs)
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408 cache[cacheKey] = data
8
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409 ci.session.close()
0
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410 return data
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411 try:
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412 # The cache key may or may not be in the cache at this point, it
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413 # /likely/ is. However we take no chances that it wasn't evicted between
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414 # when we checked above and now, so we reference the object from the
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415 # cache in preparation to return.
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416 data = cache[cacheKey]
8
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417 ci.session.close()
0
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418 return data
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419 except KeyError:
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420 # If access fails due to eviction, we will fail over and can ensure that
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421 # data is inserted.
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422 data = _list_organisms(ci, *args, **kwargs)
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423 cache[cacheKey] = data
8
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424 ci.session.close()
0
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425 return data
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426
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427
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428 def _list_organisms(ci, *args, **kwargs):
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429 # Fetch the orgs.
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430 orgs_data = []
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431 for org in ci.organism.get_organisms():
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432 clean_name = '%s %s' % (org['genus'], org['species'])
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433 if 'infraspecific_name' in org and org['infraspecific_name']:
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434 clean_name += ' (%s)' % (org['infraspecific_name'])
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435 orgs_data.append((clean_name, str(org['organism_id']), False))
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436 return orgs_data
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437
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438
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439 def list_analyses(*args, **kwargs):
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440
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441 ci = _get_instance()
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442
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443 # Key for cached data
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444 cacheKey = 'analyses'
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445 # We don't want to trust "if key in cache" because between asking and fetch
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446 # it might through key error.
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447 if cacheKey not in cache:
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448 # However if it ISN'T there, we know we're safe to fetch + put in
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449 # there.<?xml version="1.0"?>
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450
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451 data = _list_analyses(ci, *args, **kwargs)
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452 cache[cacheKey] = data
8
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453 ci.session.close()
0
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454 return data
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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455 try:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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456 # The cache key may or may not be in the cache at this point, it
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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457 # /likely/ is. However we take no chances that it wasn't evicted between
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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458 # when we checked above and now, so we reference the object from the
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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459 # cache in preparation to return.
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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460 data = cache[cacheKey]
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461 ci.session.close()
0
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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462 return data
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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463 except KeyError:
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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464 # If access fails due to eviction, we will fail over and can ensure that
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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465 # data is inserted.
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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466 data = _list_analyses(ci, *args, **kwargs)
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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467 cache[cacheKey] = data
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9867cab3574b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
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468 ci.session.close()
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e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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469 return data
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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470
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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471
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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472 def _list_analyses(ci, *args, **kwargs):
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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473 ans_data = []
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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474 for an in ci.analysis.get_analyses():
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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475 ans_data.append((an['name'], str(an['analysis_id']), False))
e2a554c9ab8b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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476 return ans_data