tripal_phylogeny_sync: tripal.py annotate

annotate tripal.py @ 0:d1f5c6c38277 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1

author	gga
date	Mon, 06 Aug 2018 04:45:30 -0400
parents
children

rev	line source
0 d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	1 import collections
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	2 import os
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	3 import time
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	4 from abc import abstractmethod
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	5
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	6 import tripal
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	7
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	8
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	9 #############################################
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	10 # BEGIN IMPORT OF CACHING LIBRARY #
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	11 #############################################
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	12 # This code is licensed under the MIT #
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	13 # License and is a copy of code publicly #
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	14 # available in rev. #
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	15 # e27332bc82f4e327aedaec17c9b656ae719322ed #
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	16 # of https://github.com/tkem/cachetools/ #
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	17 #############################################
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	18 class DefaultMapping(collections.MutableMapping):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	19
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	20 __slots__ = ()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	21
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	22 @abstractmethod
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	23 def __contains__(self, key): # pragma: nocover
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	24 return False
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	25
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	26 @abstractmethod
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	27 def __getitem__(self, key): # pragma: nocover
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	28 if hasattr(self.__class__, '__missing__'):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	29 return self.__class__.__missing__(self, key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	30 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	31 raise KeyError(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	32
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	33 def get(self, key, default=None):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	34 if key in self:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	35 return self[key]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	36 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	37 return default
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	38
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	39 __marker = object()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	40
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	41 def pop(self, key, default=__marker):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	42 if key in self:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	43 value = self[key]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	44 del self[key]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	45 elif default is self.__marker:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	46 raise KeyError(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	47 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	48 value = default
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	49 return value
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	50
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	51 def setdefault(self, key, default=None):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	52 if key in self:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	53 value = self[key]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	54 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	55 self[key] = value = default
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	56 return value
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	57
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	58
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	59 DefaultMapping.register(dict)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	60
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	61
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	62 class _DefaultSize(object):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	63 def __getitem__(self, _):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	64 return 1
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	65
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	66 def __setitem__(self, _, value):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	67 assert value == 1
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	68
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	69 def pop(self, _):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	70 return 1
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	71
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	72
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	73 class Cache(DefaultMapping):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	74 """Mutable mapping to serve as a simple cache or cache base class."""
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	75
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	76 __size = _DefaultSize()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	77
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	78 def __init__(self, maxsize, missing=None, getsizeof=None):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	79 if missing:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	80 self.__missing = missing
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	81 if getsizeof:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	82 self.__getsizeof = getsizeof
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	83 self.__size = dict()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	84 self.__data = dict()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	85 self.__currsize = 0
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	86 self.__maxsize = maxsize
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	87
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	88 def __repr__(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	89 return '%s(%r, maxsize=%r, currsize=%r)' % (
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	90 self.__class__.__name__,
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	91 list(self.__data.items()),
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	92 self.__maxsize,
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	93 self.__currsize,
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	94 )
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	95
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	96 def __getitem__(self, key):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	97 try:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	98 return self.__data[key]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	99 except KeyError:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	100 return self.__missing__(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	101
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	102 def __setitem__(self, key, value):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	103 maxsize = self.__maxsize
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	104 size = self.getsizeof(value)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	105 if size > maxsize:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	106 raise ValueError('value too large')
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	107 if key not in self.__data or self.__size[key] < size:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	108 while self.__currsize + size > maxsize:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	109 self.popitem()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	110 if key in self.__data:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	111 diffsize = size - self.__size[key]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	112 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	113 diffsize = size
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	114 self.__data[key] = value
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	115 self.__size[key] = size
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	116 self.__currsize += diffsize
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	117
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	118 def __delitem__(self, key):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	119 size = self.__size.pop(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	120 del self.__data[key]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	121 self.__currsize -= size
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	122
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	123 def __contains__(self, key):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	124 return key in self.__data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	125
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	126 def __missing__(self, key):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	127 value = self.__missing(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	128 try:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	129 self.__setitem__(key, value)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	130 except ValueError:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	131 pass # value too large
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	132 return value
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	133
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	134 def __iter__(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	135 return iter(self.__data)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	136
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	137 def __len__(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	138 return len(self.__data)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	139
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	140 @staticmethod
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	141 def __getsizeof(value):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	142 return 1
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	143
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	144 @staticmethod
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	145 def __missing(key):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	146 raise KeyError(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	147
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	148 @property
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	149 def maxsize(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	150 """The maximum size of the cache."""
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	151 return self.__maxsize
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	152
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	153 @property
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	154 def currsize(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	155 """The current size of the cache."""
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	156 return self.__currsize
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	157
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	158 def getsizeof(self, value):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	159 """Return the size of a cache element's value."""
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	160 return self.__getsizeof(value)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	161
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	162
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	163 class _Link(object):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	164
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	165 __slots__ = ('key', 'expire', 'next', 'prev')
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	166
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	167 def __init__(self, key=None, expire=None):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	168 self.key = key
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	169 self.expire = expire
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	170
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	171 def __reduce__(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	172 return _Link, (self.key, self.expire)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	173
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	174 def unlink(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	175 next = self.next
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	176 prev = self.prev
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	177 prev.next = next
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	178 next.prev = prev
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	179
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	180
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	181 class _Timer(object):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	182
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	183 def __init__(self, timer):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	184 self.__timer = timer
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	185 self.__nesting = 0
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	186
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	187 def __call__(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	188 if self.__nesting == 0:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	189 return self.__timer()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	190 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	191 return self.__time
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	192
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	193 def __enter__(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	194 if self.__nesting == 0:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	195 self.__time = time = self.__timer()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	196 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	197 time = self.__time
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	198 self.__nesting += 1
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	199 return time
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	200
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	201 def __exit__(self, *exc):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	202 self.__nesting -= 1
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	203
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	204 def __reduce__(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	205 return _Timer, (self.__timer,)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	206
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	207 def __getattr__(self, name):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	208 return getattr(self.__timer, name)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	209
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	210
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	211 class TTLCache(Cache):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	212 """LRU Cache implementation with per-item time-to-live (TTL) value."""
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	213
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	214 def __init__(self, maxsize, ttl, timer=time.time, missing=None,
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	215 getsizeof=None):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	216 Cache.__init__(self, maxsize, missing, getsizeof)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	217 self.__root = root = _Link()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	218 root.prev = root.next = root
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	219 self.__links = collections.OrderedDict()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	220 self.__timer = _Timer(timer)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	221 self.__ttl = ttl
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	222
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	223 def __contains__(self, key):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	224 try:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	225 link = self.__links[key] # no reordering
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	226 except KeyError:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	227 return False
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	228 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	229 return not (link.expire < self.__timer())
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	230
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	231 def __getitem__(self, key, cache_getitem=Cache.__getitem__):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	232 try:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	233 link = self.__getlink(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	234 except KeyError:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	235 expired = False
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	236 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	237 expired = link.expire < self.__timer()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	238 if expired:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	239 return self.__missing__(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	240 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	241 return cache_getitem(self, key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	242
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	243 def __setitem__(self, key, value, cache_setitem=Cache.__setitem__):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	244 with self.__timer as time:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	245 self.expire(time)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	246 cache_setitem(self, key, value)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	247 try:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	248 link = self.__getlink(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	249 except KeyError:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	250 self.__links[key] = link = _Link(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	251 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	252 link.unlink()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	253 link.expire = time + self.__ttl
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	254 link.next = root = self.__root
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	255 link.prev = prev = root.prev
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	256 prev.next = root.prev = link
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	257
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	258 def __delitem__(self, key, cache_delitem=Cache.__delitem__):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	259 cache_delitem(self, key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	260 link = self.__links.pop(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	261 link.unlink()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	262 if link.expire < self.__timer():
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	263 raise KeyError(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	264
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	265 def __iter__(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	266 root = self.__root
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	267 curr = root.next
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	268 while curr is not root:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	269 # "freeze" time for iterator access
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	270 with self.__timer as time:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	271 if not (curr.expire < time):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	272 yield curr.key
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	273 curr = curr.next
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	274
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	275 def __len__(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	276 root = self.__root
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	277 curr = root.next
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	278 time = self.__timer()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	279 count = len(self.__links)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	280 while curr is not root and curr.expire < time:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	281 count -= 1
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	282 curr = curr.next
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	283 return count
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	284
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	285 def __setstate__(self, state):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	286 self.__dict__.update(state)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	287 root = self.__root
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	288 root.prev = root.next = root
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	289 for link in sorted(self.__links.values(), key=lambda obj: obj.expire):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	290 link.next = root
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	291 link.prev = prev = root.prev
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	292 prev.next = root.prev = link
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	293 self.expire(self.__timer())
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	294
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	295 def __repr__(self, cache_repr=Cache.__repr__):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	296 with self.__timer as time:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	297 self.expire(time)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	298 return cache_repr(self)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	299
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	300 @property
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	301 def currsize(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	302 with self.__timer as time:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	303 self.expire(time)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	304 return super(TTLCache, self).currsize
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	305
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	306 @property
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	307 def timer(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	308 """The timer function used by the cache."""
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	309 return self.__timer
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	310
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	311 @property
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	312 def ttl(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	313 """The time-to-live value of the cache's items."""
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	314 return self.__ttl
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	315
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	316 def expire(self, time=None):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	317 """Remove expired items from the cache."""
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	318 if time is None:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	319 time = self.__timer()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	320 root = self.__root
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	321 curr = root.next
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	322 links = self.__links
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	323 cache_delitem = Cache.__delitem__
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	324 while curr is not root and curr.expire < time:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	325 cache_delitem(self, curr.key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	326 del links[curr.key]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	327 next = curr.next
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	328 curr.unlink()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	329 curr = next
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	330
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	331 def clear(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	332 with self.__timer as time:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	333 self.expire(time)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	334 Cache.clear(self)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	335
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	336 def get(self, args, *kwargs):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	337 with self.__timer:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	338 return Cache.get(self, args, *kwargs)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	339
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	340 def pop(self, args, *kwargs):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	341 with self.__timer:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	342 return Cache.pop(self, args, *kwargs)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	343
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	344 def setdefault(self, args, *kwargs):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	345 with self.__timer:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	346 return Cache.setdefault(self, args, *kwargs)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	347
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	348 def popitem(self):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	349 """Remove and return the `(key, value)` pair least recently used that
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	350 has not already expired.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	351
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	352 """
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	353 with self.__timer as time:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	354 self.expire(time)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	355 try:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	356 key = next(iter(self.__links))
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	357 except StopIteration:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	358 raise KeyError('%s is empty' % self.__class__.__name__)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	359 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	360 return (key, self.pop(key))
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	361
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	362 if hasattr(collections.OrderedDict, 'move_to_end'):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	363 def __getlink(self, key):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	364 value = self.__links[key]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	365 self.__links.move_to_end(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	366 return value
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	367 else:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	368 def __getlink(self, key):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	369 value = self.__links.pop(key)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	370 self.__links[key] = value
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	371 return value
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	372
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	373
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	374 #############################################
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	375 # END IMPORT OF CACHING LIBRARY #
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	376 #############################################
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	377
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	378 cache = TTLCache(
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	379 100, # Up to 100 items
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	380 1 * 60 # 5 minute cache life
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	381 )
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	382
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	383
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	384 def _get_instance():
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	385 return tripal.TripalInstance(
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	386 os.environ['GALAXY_TRIPAL_URL'],
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	387 os.environ['GALAXY_TRIPAL_USER'],
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	388 os.environ['GALAXY_TRIPAL_PASSWORD']
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	389 )
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	390
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	391
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	392 def list_organisms(args, *kwargs):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	393
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	394 ti = _get_instance()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	395
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	396 # Key for cached data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	397 cacheKey = 'orgs'
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	398 # We don't want to trust "if key in cache" because between asking and fetch
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	399 # it might through key error.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	400 if cacheKey not in cache:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	401 # However if it ISN'T there, we know we're safe to fetch + put in
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	402 # there.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	403 data = _list_organisms(ti, args, *kwargs)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	404 cache[cacheKey] = data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	405 return data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	406 try:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	407 # The cache key may or may not be in the cache at this point, it
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	408 # /likely/ is. However we take no chances that it wasn't evicted between
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	409 # when we checked above and now, so we reference the object from the
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	410 # cache in preparation to return.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	411 data = cache[cacheKey]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	412 return data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	413 except KeyError:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	414 # If access fails due to eviction, we will fail over and can ensure that
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	415 # data is inserted.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	416 data = _list_organisms(ti, args, *kwargs)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	417 cache[cacheKey] = data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	418 return data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	419
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	420
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	421 def _list_organisms(ti, args, *kwargs):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	422 # Fetch the orgs.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	423 orgs_data = []
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	424 for org in ti.organism.get_organisms():
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	425 clean_name = '%s %s' % (org['genus'], org['species'])
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	426 if org['infraspecific_name']:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	427 clean_name += ' (%s)' % (org['infraspecific_name'])
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	428 orgs_data.append((clean_name, org['organism_id'], False))
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	429 return orgs_data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	430
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	431
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	432 def list_analyses(args, *kwargs):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	433
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	434 ti = _get_instance()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	435
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	436 # Key for cached data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	437 cacheKey = 'analyses'
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	438 # We don't want to trust "if key in cache" because between asking and fetch
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	439 # it might through key error.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	440 if cacheKey not in cache:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	441 # However if it ISN'T there, we know we're safe to fetch + put in
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	442 # there.<?xml version="1.0"?>
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	443
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	444 data = _list_analyses(ti, args, *kwargs)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	445 cache[cacheKey] = data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	446 return data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	447 try:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	448 # The cache key may or may not be in the cache at this point, it
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	449 # /likely/ is. However we take no chances that it wasn't evicted between
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	450 # when we checked above and now, so we reference the object from the
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	451 # cache in preparation to return.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	452 data = cache[cacheKey]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	453 return data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	454 except KeyError:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	455 # If access fails due to eviction, we will fail over and can ensure that
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	456 # data is inserted.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	457 data = _list_analyses(ti, args, *kwargs)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	458 cache[cacheKey] = data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	459 return data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	460
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	461
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	462 def _list_analyses(ti, args, *kwargs):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	463 ans_data = []
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	464 for an in ti.analysis.get_analyses():
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	465 ans_data.append((an['name'], an['analysis_id'], False))
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	466 return ans_data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	467
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	468
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	469 def list_blastdbs(args, *kwargs):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	470
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	471 ti = _get_instance()
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	472
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	473 # Key for cached data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	474 cacheKey = 'blastdbs'
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	475 # We don't want to trust "if key in cache" because between asking and fetch
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	476 # it might through key error.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	477 if cacheKey not in cache:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	478 # However if it ISN'T there, we know we're safe to fetch + put in
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	479 # there.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	480 data = _list_blastdbs(ti, args, *kwargs)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	481 cache[cacheKey] = data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	482 return data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	483 try:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	484 # The cache key may or may not be in the cache at this point, it
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	485 # /likely/ is. However we take no chances that it wasn't evicted between
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	486 # when we checked above and now, so we reference the object from the
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	487 # cache in preparation to return.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	488 data = cache[cacheKey]
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	489 return data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	490 except KeyError:
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	491 # If access fails due to eviction, we will fail over and can ensure that
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	492 # data is inserted.
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	493 data = _list_blastdbs(ti, args, *kwargs)
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	494 cache[cacheKey] = data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	495 return data
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	496
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	497
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	498 def _list_blastdbs(ti, args, *kwargs):
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	499 dbs_data = []
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	500 for db in ti.db.get_dbs():
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	501 dbs_data.append((db['name'], db['db_id'], False))
d1f5c6c38277 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1 gga parents: diff changeset	502 return dbs_data

Mercurial > repos > gga > tripal_phylogeny_sync

annotate tripal.py @ 0:d1f5c6c38277 draft