Mercurial > repos > gga > tripal_analysis_load_fasta

annotate tripal.py @ 0:ca1eb54c95d6 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:50:45 -0400
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children 0fbe72b81b9e
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ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
1 import collections
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 import os
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3 import time
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4
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5 from abc import abstractmethod
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6
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7 import tripal
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8
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9
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10 #############################################
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11 # BEGIN IMPORT OF CACHING LIBRARY #
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12 #############################################
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13 # This code is licensed under the MIT #
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14 # License and is a copy of code publicly #
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15 # available in rev. #
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16 # e27332bc82f4e327aedaec17c9b656ae719322ed #
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17 # of https://github.com/tkem/cachetools/ #
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18 #############################################
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19 class DefaultMapping(collections.MutableMapping):
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20
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21 __slots__ = ()
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22
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23 @abstractmethod
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24 def __contains__(self, key): # pragma: nocover
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25 return False
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26
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27 @abstractmethod
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28 def __getitem__(self, key): # pragma: nocover
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29 if hasattr(self.__class__, '__missing__'):
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30 return self.__class__.__missing__(self, key)
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31 else:
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32 raise KeyError(key)
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33
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34 def get(self, key, default=None):
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35 if key in self:
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36 return self[key]
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37 else:
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38 return default
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39
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40 __marker = object()
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41
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42 def pop(self, key, default=__marker):
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43 if key in self:
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44 value = self[key]
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45 del self[key]
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46 elif default is self.__marker:
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47 raise KeyError(key)
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48 else:
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49 value = default
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50 return value
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51
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52 def setdefault(self, key, default=None):
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53 if key in self:
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54 value = self[key]
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55 else:
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56 self[key] = value = default
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57 return value
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58
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59
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60 DefaultMapping.register(dict)
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62
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63 class _DefaultSize(object):
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64 def __getitem__(self, _):
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65 return 1
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66
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67 def __setitem__(self, _, value):
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68 assert value == 1
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69
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70 def pop(self, _):
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71 return 1
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72
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73
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74 class Cache(DefaultMapping):
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75 """Mutable mapping to serve as a simple cache or cache base class."""
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76
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77 __size = _DefaultSize()
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78
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79 def __init__(self, maxsize, missing=None, getsizeof=None):
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80 if missing:
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81 self.__missing = missing
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82 if getsizeof:
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83 self.__getsizeof = getsizeof
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84 self.__size = dict()
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85 self.__data = dict()
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86 self.__currsize = 0
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87 self.__maxsize = maxsize
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88
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89 def __repr__(self):
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90 return '%s(%r, maxsize=%r, currsize=%r)' % (
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91 self.__class__.__name__,
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92 list(self.__data.items()),
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93 self.__maxsize,
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94 self.__currsize,
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95 )
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96
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97 def __getitem__(self, key):
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98 try:
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99 return self.__data[key]
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100 except KeyError:
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101 return self.__missing__(key)
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102
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103 def __setitem__(self, key, value):
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104 maxsize = self.__maxsize
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105 size = self.getsizeof(value)
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106 if size > maxsize:
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107 raise ValueError('value too large')
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108 if key not in self.__data or self.__size[key] < size:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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109 while self.__currsize + size > maxsize:
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110 self.popitem()
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111 if key in self.__data:
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112 diffsize = size - self.__size[key]
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113 else:
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114 diffsize = size
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115 self.__data[key] = value
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116 self.__size[key] = size
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117 self.__currsize += diffsize
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118
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119 def __delitem__(self, key):
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120 size = self.__size.pop(key)
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121 del self.__data[key]
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122 self.__currsize -= size
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123
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124 def __contains__(self, key):
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125 return key in self.__data
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126
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127 def __missing__(self, key):
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128 value = self.__missing(key)
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129 try:
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130 self.__setitem__(key, value)
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131 except ValueError:
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132 pass # value too large
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133 return value
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134
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135 def __iter__(self):
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136 return iter(self.__data)
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137
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138 def __len__(self):
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139 return len(self.__data)
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140
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141 @staticmethod
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142 def __getsizeof(value):
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143 return 1
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144
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145 @staticmethod
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146 def __missing(key):
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147 raise KeyError(key)
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148
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149 @property
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150 def maxsize(self):
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151 """The maximum size of the cache."""
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152 return self.__maxsize
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153
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154 @property
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155 def currsize(self):
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156 """The current size of the cache."""
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157 return self.__currsize
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158
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159 def getsizeof(self, value):
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160 """Return the size of a cache element's value."""
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161 return self.__getsizeof(value)
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162
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163
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164 class _Link(object):
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165
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166 __slots__ = ('key', 'expire', 'next', 'prev')
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167
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168 def __init__(self, key=None, expire=None):
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169 self.key = key
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170 self.expire = expire
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171
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172 def __reduce__(self):
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173 return _Link, (self.key, self.expire)
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174
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175 def unlink(self):
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176 next = self.next
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177 prev = self.prev
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178 prev.next = next
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179 next.prev = prev
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180
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181
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182 class _Timer(object):
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183
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184 def __init__(self, timer):
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185 self.__timer = timer
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186 self.__nesting = 0
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187
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
188 def __call__(self):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
189 if self.__nesting == 0:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
190 return self.__timer()
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
191 else:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
192 return self.__time
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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193
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
194 def __enter__(self):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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195 if self.__nesting == 0:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
196 self.__time = time = self.__timer()
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
197 else:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
198 time = self.__time
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
199 self.__nesting += 1
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
200 return time
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
201
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
202 def __exit__(self, *exc):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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203 self.__nesting -= 1
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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204
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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205 def __reduce__(self):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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206 return _Timer, (self.__timer,)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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207
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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208 def __getattr__(self, name):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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209 return getattr(self.__timer, name)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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210
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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211
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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212 class TTLCache(Cache):
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213 """LRU Cache implementation with per-item time-to-live (TTL) value."""
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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214
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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215 def __init__(self, maxsize, ttl, timer=time.time, missing=None,
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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216 getsizeof=None):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
217 Cache.__init__(self, maxsize, missing, getsizeof)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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218 self.__root = root = _Link()
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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219 root.prev = root.next = root
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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220 self.__links = collections.OrderedDict()
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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221 self.__timer = _Timer(timer)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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222 self.__ttl = ttl
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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223
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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224 def __contains__(self, key):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
225 try:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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226 link = self.__links[key] # no reordering
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
227 except KeyError:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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228 return False
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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229 else:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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230 return not (link.expire < self.__timer())
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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231
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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232 def __getitem__(self, key, cache_getitem=Cache.__getitem__):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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233 try:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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234 link = self.__getlink(key)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
235 except KeyError:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
236 expired = False
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
237 else:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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238 expired = link.expire < self.__timer()
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
239 if expired:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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240 return self.__missing__(key)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
241 else:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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242 return cache_getitem(self, key)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
243
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
244 def __setitem__(self, key, value, cache_setitem=Cache.__setitem__):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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245 with self.__timer as time:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
246 self.expire(time)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
247 cache_setitem(self, key, value)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
248 try:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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249 link = self.__getlink(key)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
250 except KeyError:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
251 self.__links[key] = link = _Link(key)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
252 else:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
253 link.unlink()
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
254 link.expire = time + self.__ttl
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
255 link.next = root = self.__root
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
256 link.prev = prev = root.prev
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
257 prev.next = root.prev = link
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
258
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
259 def __delitem__(self, key, cache_delitem=Cache.__delitem__):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
260 cache_delitem(self, key)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
261 link = self.__links.pop(key)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
262 link.unlink()
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
263 if link.expire < self.__timer():
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
264 raise KeyError(key)
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
265
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
266 def __iter__(self):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
267 root = self.__root
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
268 curr = root.next
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
269 while curr is not root:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
270 # "freeze" time for iterator access
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
271 with self.__timer as time:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
272 if not (curr.expire < time):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
273 yield curr.key
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
274 curr = curr.next
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
275
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
276 def __len__(self):
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
277 root = self.__root
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
278 curr = root.next
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
parents:
diff changeset
279 time = self.__timer()
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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parents:
diff changeset
280 count = len(self.__links)
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281 while curr is not root and curr.expire < time:
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282 count -= 1
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283 curr = curr.next
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284 return count
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285
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286 def __setstate__(self, state):
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287 self.__dict__.update(state)
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288 root = self.__root
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289 root.prev = root.next = root
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290 for link in sorted(self.__links.values(), key=lambda obj: obj.expire):
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291 link.next = root
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292 link.prev = prev = root.prev
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293 prev.next = root.prev = link
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294 self.expire(self.__timer())
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295
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296 def __repr__(self, cache_repr=Cache.__repr__):
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297 with self.__timer as time:
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298 self.expire(time)
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299 return cache_repr(self)
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300
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301 @property
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302 def currsize(self):
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303 with self.__timer as time:
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304 self.expire(time)
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305 return super(TTLCache, self).currsize
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306
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307 @property
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308 def timer(self):
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309 """The timer function used by the cache."""
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310 return self.__timer
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311
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312 @property
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313 def ttl(self):
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314 """The time-to-live value of the cache's items."""
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315 return self.__ttl
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316
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317 def expire(self, time=None):
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318 """Remove expired items from the cache."""
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319 if time is None:
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320 time = self.__timer()
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321 root = self.__root
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322 curr = root.next
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323 links = self.__links
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324 cache_delitem = Cache.__delitem__
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325 while curr is not root and curr.expire < time:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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326 cache_delitem(self, curr.key)
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327 del links[curr.key]
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328 next = curr.next
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329 curr.unlink()
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330 curr = next
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331
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332 def clear(self):
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333 with self.__timer as time:
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334 self.expire(time)
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diff changeset
335 Cache.clear(self)
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336
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337 def get(self, *args, **kwargs):
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338 with self.__timer:
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339 return Cache.get(self, *args, **kwargs)
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340
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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341 def pop(self, *args, **kwargs):
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342 with self.__timer:
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343 return Cache.pop(self, *args, **kwargs)
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344
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345 def setdefault(self, *args, **kwargs):
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346 with self.__timer:
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347 return Cache.setdefault(self, *args, **kwargs)
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348
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349 def popitem(self):
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350 """Remove and return the `(key, value)` pair least recently used that
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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351 has not already expired.
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352
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353 """
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354 with self.__timer as time:
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355 self.expire(time)
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diff changeset
356 try:
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357 key = next(iter(self.__links))
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358 except StopIteration:
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359 raise KeyError('%s is empty' % self.__class__.__name__)
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diff changeset
360 else:
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361 return (key, self.pop(key))
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diff changeset
362
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363 if hasattr(collections.OrderedDict, 'move_to_end'):
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364 def __getlink(self, key):
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365 value = self.__links[key]
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366 self.__links.move_to_end(key)
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diff changeset
367 return value
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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368 else:
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369 def __getlink(self, key):
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370 value = self.__links.pop(key)
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diff changeset
371 self.__links[key] = value
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diff changeset
372 return value
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373
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374
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375 #############################################
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376 # END IMPORT OF CACHING LIBRARY #
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377 #############################################
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378
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379 cache = TTLCache(
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380 100, # Up to 100 items
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381 1 * 60 # 5 minute cache life
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382 )
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383
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384
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385 def _get_instance():
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386 return tripal.TripalInstance(
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387 os.environ['GALAXY_TRIPAL_URL'],
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388 os.environ['GALAXY_TRIPAL_USER'],
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389 os.environ['GALAXY_TRIPAL_PASSWORD']
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390 )
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391
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392
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393 def list_organisms(*args, **kwargs):
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394
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395 ti = _get_instance()
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396
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397 # Key for cached data
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398 cacheKey = 'orgs'
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399 # We don't want to trust "if key in cache" because between asking and fetch
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400 # it might through key error.
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401 if cacheKey not in cache:
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402 # However if it ISN'T there, we know we're safe to fetch + put in
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403 # there.
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404 data = _list_organisms(ti, *args, **kwargs)
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405 cache[cacheKey] = data
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406 return data
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407 try:
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408 # The cache key may or may not be in the cache at this point, it
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409 # /likely/ is. However we take no chances that it wasn't evicted between
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410 # when we checked above and now, so we reference the object from the
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411 # cache in preparation to return.
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412 data = cache[cacheKey]
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413 return data
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414 except KeyError:
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415 # If access fails due to eviction, we will fail over and can ensure that
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416 # data is inserted.
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417 data = _list_organisms(ti, *args, **kwargs)
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418 cache[cacheKey] = data
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419 return data
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420
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421
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422 def _list_organisms(ti, *args, **kwargs):
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423 # Fetch the orgs.
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424 orgs_data = []
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425 for org in ti.organism.get_organisms():
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426 clean_name = '%s %s' % (org['genus'], org['species'])
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427 if org['infraspecific_name']:
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428 clean_name += ' (%s)' % (org['infraspecific_name'])
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429 orgs_data.append((clean_name, org['organism_id'], False))
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430 return orgs_data
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431
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432
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433 def list_analyses(*args, **kwargs):
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434
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435 ti = _get_instance()
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436
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437 # Key for cached data
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438 cacheKey = 'analyses'
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439 # We don't want to trust "if key in cache" because between asking and fetch
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440 # it might through key error.
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441 if cacheKey not in cache:
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442 # However if it ISN'T there, we know we're safe to fetch + put in
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443 # there.<?xml version="1.0"?>
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444
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445 data = _list_analyses(ti, *args, **kwargs)
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446 cache[cacheKey] = data
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447 return data
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448 try:
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449 # The cache key may or may not be in the cache at this point, it
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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450 # /likely/ is. However we take no chances that it wasn't evicted between
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451 # when we checked above and now, so we reference the object from the
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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452 # cache in preparation to return.
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453 data = cache[cacheKey]
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454 return data
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455 except KeyError:
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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456 # If access fails due to eviction, we will fail over and can ensure that
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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457 # data is inserted.
ca1eb54c95d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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458 data = _list_analyses(ti, *args, **kwargs)
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459 cache[cacheKey] = data
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diff changeset
460 return data
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461
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462
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463 def _list_analyses(ti, *args, **kwargs):
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464 ans_data = []
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465 for an in ti.analysis.get_analyses():
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466 ans_data.append((an['name'], an['analysis_id'], False))
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467 return ans_data
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468
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469
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470 def list_blastdbs(*args, **kwargs):
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471
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472 ti = _get_instance()
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473
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474 # Key for cached data
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475 cacheKey = 'blastdbs'
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476 # We don't want to trust "if key in cache" because between asking and fetch
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477 # it might through key error.
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478 if cacheKey not in cache:
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479 # However if it ISN'T there, we know we're safe to fetch + put in
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480 # there.
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481 data = _list_blastdbs(ti, *args, **kwargs)
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482 cache[cacheKey] = data
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483 return data
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484 try:
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485 # The cache key may or may not be in the cache at this point, it
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486 # /likely/ is. However we take no chances that it wasn't evicted between
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487 # when we checked above and now, so we reference the object from the
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488 # cache in preparation to return.
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489 data = cache[cacheKey]
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490 return data
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491 except KeyError:
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492 # If access fails due to eviction, we will fail over and can ensure that
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493 # data is inserted.
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494 data = _list_blastdbs(ti, *args, **kwargs)
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495 cache[cacheKey] = data
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496 return data
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497
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498
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499 def _list_blastdbs(ti, *args, **kwargs):
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500 dbs_data = []
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501 for db in ti.db.get_dbs():
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502 dbs_data.append((db['name'], db['db_id'], False))
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503 return dbs_data