tripal_analysis_load_blast: tripal.py annotate

annotate tripal.py @ 0:e1d4fad18572 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268

author	gga
date	Mon, 11 Sep 2017 05:50:16 -0400
parents
children	bd4d410ac108

rev	line source
0 e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	1 import collections
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	2 import os
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	3 import time
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	4
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	5 from abc import abstractmethod
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	6
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	7 import tripal
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	8
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	9
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	10 #############################################
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	11 # BEGIN IMPORT OF CACHING LIBRARY #
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	12 #############################################
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	13 # This code is licensed under the MIT #
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	14 # License and is a copy of code publicly #
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	15 # available in rev. #
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	16 # e27332bc82f4e327aedaec17c9b656ae719322ed #
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	17 # of https://github.com/tkem/cachetools/ #
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	18 #############################################
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	19 class DefaultMapping(collections.MutableMapping):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	20
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	21 __slots__ = ()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	22
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	23 @abstractmethod
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	24 def __contains__(self, key): # pragma: nocover
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	25 return False
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	26
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	27 @abstractmethod
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	28 def __getitem__(self, key): # pragma: nocover
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	29 if hasattr(self.__class__, '__missing__'):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	30 return self.__class__.__missing__(self, key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	31 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	32 raise KeyError(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	33
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	34 def get(self, key, default=None):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	35 if key in self:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	36 return self[key]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	37 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	38 return default
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	39
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	40 __marker = object()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	41
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	42 def pop(self, key, default=__marker):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	43 if key in self:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	44 value = self[key]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	45 del self[key]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	46 elif default is self.__marker:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	47 raise KeyError(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	48 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	49 value = default
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	50 return value
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	51
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	52 def setdefault(self, key, default=None):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	53 if key in self:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	54 value = self[key]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	55 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	56 self[key] = value = default
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	57 return value
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	58
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	59
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	60 DefaultMapping.register(dict)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	61
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	62
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	63 class _DefaultSize(object):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	64 def __getitem__(self, _):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	65 return 1
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	66
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	67 def __setitem__(self, _, value):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	68 assert value == 1
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	69
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	70 def pop(self, _):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	71 return 1
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	72
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	73
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	74 class Cache(DefaultMapping):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	75 """Mutable mapping to serve as a simple cache or cache base class."""
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	76
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	77 __size = _DefaultSize()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	78
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	79 def __init__(self, maxsize, missing=None, getsizeof=None):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	80 if missing:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	81 self.__missing = missing
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	82 if getsizeof:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	83 self.__getsizeof = getsizeof
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	84 self.__size = dict()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	85 self.__data = dict()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	86 self.__currsize = 0
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	87 self.__maxsize = maxsize
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	88
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	89 def __repr__(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	90 return '%s(%r, maxsize=%r, currsize=%r)' % (
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	91 self.__class__.__name__,
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	92 list(self.__data.items()),
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	93 self.__maxsize,
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	94 self.__currsize,
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	95 )
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	96
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	97 def __getitem__(self, key):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	98 try:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	99 return self.__data[key]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	100 except KeyError:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	101 return self.__missing__(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	102
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	103 def __setitem__(self, key, value):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	104 maxsize = self.__maxsize
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	105 size = self.getsizeof(value)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	106 if size > maxsize:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	107 raise ValueError('value too large')
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	108 if key not in self.__data or self.__size[key] < size:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	109 while self.__currsize + size > maxsize:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	110 self.popitem()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	111 if key in self.__data:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	112 diffsize = size - self.__size[key]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	113 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	114 diffsize = size
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	115 self.__data[key] = value
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	116 self.__size[key] = size
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	117 self.__currsize += diffsize
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	118
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	119 def __delitem__(self, key):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	120 size = self.__size.pop(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	121 del self.__data[key]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	122 self.__currsize -= size
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	123
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	124 def __contains__(self, key):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	125 return key in self.__data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	126
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	127 def __missing__(self, key):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	128 value = self.__missing(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	129 try:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	130 self.__setitem__(key, value)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	131 except ValueError:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	132 pass # value too large
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	133 return value
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	134
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	135 def __iter__(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	136 return iter(self.__data)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	137
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	138 def __len__(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	139 return len(self.__data)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	140
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	141 @staticmethod
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	142 def __getsizeof(value):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	143 return 1
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	144
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	145 @staticmethod
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	146 def __missing(key):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	147 raise KeyError(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	148
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	149 @property
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	150 def maxsize(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	151 """The maximum size of the cache."""
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	152 return self.__maxsize
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	153
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	154 @property
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	155 def currsize(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	156 """The current size of the cache."""
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	157 return self.__currsize
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	158
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	159 def getsizeof(self, value):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	160 """Return the size of a cache element's value."""
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	161 return self.__getsizeof(value)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	162
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	163
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	164 class _Link(object):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	165
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	166 __slots__ = ('key', 'expire', 'next', 'prev')
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	167
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	168 def __init__(self, key=None, expire=None):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	169 self.key = key
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	170 self.expire = expire
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	171
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	172 def __reduce__(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	173 return _Link, (self.key, self.expire)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	174
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	175 def unlink(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	176 next = self.next
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	177 prev = self.prev
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	178 prev.next = next
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	179 next.prev = prev
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	180
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	181
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	182 class _Timer(object):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	183
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	184 def __init__(self, timer):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	185 self.__timer = timer
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	186 self.__nesting = 0
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	187
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	188 def __call__(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	189 if self.__nesting == 0:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	190 return self.__timer()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	191 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	192 return self.__time
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	193
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	194 def __enter__(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	195 if self.__nesting == 0:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	196 self.__time = time = self.__timer()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	197 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	198 time = self.__time
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	199 self.__nesting += 1
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	200 return time
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	201
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	202 def __exit__(self, *exc):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	203 self.__nesting -= 1
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	204
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	205 def __reduce__(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	206 return _Timer, (self.__timer,)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	207
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	208 def __getattr__(self, name):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	209 return getattr(self.__timer, name)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	210
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	211
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	212 class TTLCache(Cache):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	213 """LRU Cache implementation with per-item time-to-live (TTL) value."""
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	214
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	215 def __init__(self, maxsize, ttl, timer=time.time, missing=None,
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	216 getsizeof=None):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	217 Cache.__init__(self, maxsize, missing, getsizeof)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	218 self.__root = root = _Link()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	219 root.prev = root.next = root
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	220 self.__links = collections.OrderedDict()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	221 self.__timer = _Timer(timer)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	222 self.__ttl = ttl
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	223
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	224 def __contains__(self, key):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	225 try:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	226 link = self.__links[key] # no reordering
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	227 except KeyError:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	228 return False
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	229 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	230 return not (link.expire < self.__timer())
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	231
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	232 def __getitem__(self, key, cache_getitem=Cache.__getitem__):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	233 try:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	234 link = self.__getlink(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	235 except KeyError:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	236 expired = False
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	237 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	238 expired = link.expire < self.__timer()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	239 if expired:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	240 return self.__missing__(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	241 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	242 return cache_getitem(self, key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	243
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	244 def __setitem__(self, key, value, cache_setitem=Cache.__setitem__):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	245 with self.__timer as time:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	246 self.expire(time)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	247 cache_setitem(self, key, value)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	248 try:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	249 link = self.__getlink(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	250 except KeyError:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	251 self.__links[key] = link = _Link(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	252 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	253 link.unlink()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	254 link.expire = time + self.__ttl
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	255 link.next = root = self.__root
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	256 link.prev = prev = root.prev
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	257 prev.next = root.prev = link
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	258
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	259 def __delitem__(self, key, cache_delitem=Cache.__delitem__):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	260 cache_delitem(self, key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	261 link = self.__links.pop(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	262 link.unlink()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	263 if link.expire < self.__timer():
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	264 raise KeyError(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	265
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	266 def __iter__(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	267 root = self.__root
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	268 curr = root.next
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	269 while curr is not root:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	270 # "freeze" time for iterator access
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	271 with self.__timer as time:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	272 if not (curr.expire < time):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	273 yield curr.key
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	274 curr = curr.next
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	275
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	276 def __len__(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	277 root = self.__root
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	278 curr = root.next
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	279 time = self.__timer()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	280 count = len(self.__links)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	281 while curr is not root and curr.expire < time:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	282 count -= 1
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	283 curr = curr.next
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	284 return count
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	285
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	286 def __setstate__(self, state):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	287 self.__dict__.update(state)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	288 root = self.__root
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	289 root.prev = root.next = root
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	290 for link in sorted(self.__links.values(), key=lambda obj: obj.expire):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	291 link.next = root
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	292 link.prev = prev = root.prev
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	293 prev.next = root.prev = link
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	294 self.expire(self.__timer())
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	295
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	296 def __repr__(self, cache_repr=Cache.__repr__):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	297 with self.__timer as time:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	298 self.expire(time)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	299 return cache_repr(self)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	300
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	301 @property
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	302 def currsize(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	303 with self.__timer as time:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	304 self.expire(time)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	305 return super(TTLCache, self).currsize
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	306
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	307 @property
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	308 def timer(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	309 """The timer function used by the cache."""
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	310 return self.__timer
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	311
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	312 @property
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	313 def ttl(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	314 """The time-to-live value of the cache's items."""
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	315 return self.__ttl
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	316
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	317 def expire(self, time=None):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	318 """Remove expired items from the cache."""
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	319 if time is None:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	320 time = self.__timer()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	321 root = self.__root
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	322 curr = root.next
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	323 links = self.__links
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	324 cache_delitem = Cache.__delitem__
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	325 while curr is not root and curr.expire < time:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	326 cache_delitem(self, curr.key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	327 del links[curr.key]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	328 next = curr.next
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	329 curr.unlink()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	330 curr = next
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	331
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	332 def clear(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	333 with self.__timer as time:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	334 self.expire(time)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	335 Cache.clear(self)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	336
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	337 def get(self, args, *kwargs):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	338 with self.__timer:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	339 return Cache.get(self, args, *kwargs)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	340
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	341 def pop(self, args, *kwargs):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	342 with self.__timer:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	343 return Cache.pop(self, args, *kwargs)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	344
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	345 def setdefault(self, args, *kwargs):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	346 with self.__timer:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	347 return Cache.setdefault(self, args, *kwargs)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	348
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	349 def popitem(self):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	350 """Remove and return the `(key, value)` pair least recently used that
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	351 has not already expired.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	352
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	353 """
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	354 with self.__timer as time:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	355 self.expire(time)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	356 try:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	357 key = next(iter(self.__links))
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	358 except StopIteration:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	359 raise KeyError('%s is empty' % self.__class__.__name__)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	360 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	361 return (key, self.pop(key))
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	362
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	363 if hasattr(collections.OrderedDict, 'move_to_end'):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	364 def __getlink(self, key):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	365 value = self.__links[key]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	366 self.__links.move_to_end(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	367 return value
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	368 else:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	369 def __getlink(self, key):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	370 value = self.__links.pop(key)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	371 self.__links[key] = value
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	372 return value
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	373
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	374
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	375 #############################################
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	376 # END IMPORT OF CACHING LIBRARY #
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	377 #############################################
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	378
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	379 cache = TTLCache(
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	380 100, # Up to 100 items
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	381 1 * 60 # 5 minute cache life
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	382 )
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	383
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	384
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	385 def _get_instance():
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	386 return tripal.TripalInstance(
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	387 os.environ['GALAXY_TRIPAL_URL'],
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	388 os.environ['GALAXY_TRIPAL_USER'],
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	389 os.environ['GALAXY_TRIPAL_PASSWORD']
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	390 )
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	391
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	392
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	393 def list_organisms(args, *kwargs):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	394
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	395 ti = _get_instance()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	396
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	397 # Key for cached data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	398 cacheKey = 'orgs'
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	399 # We don't want to trust "if key in cache" because between asking and fetch
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	400 # it might through key error.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	401 if cacheKey not in cache:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	402 # However if it ISN'T there, we know we're safe to fetch + put in
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	403 # there.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	404 data = _list_organisms(ti, args, *kwargs)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	405 cache[cacheKey] = data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	406 return data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	407 try:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	408 # The cache key may or may not be in the cache at this point, it
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	409 # /likely/ is. However we take no chances that it wasn't evicted between
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	410 # when we checked above and now, so we reference the object from the
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	411 # cache in preparation to return.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	412 data = cache[cacheKey]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	413 return data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	414 except KeyError:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	415 # If access fails due to eviction, we will fail over and can ensure that
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	416 # data is inserted.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	417 data = _list_organisms(ti, args, *kwargs)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	418 cache[cacheKey] = data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	419 return data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	420
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	421
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	422 def _list_organisms(ti, args, *kwargs):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	423 # Fetch the orgs.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	424 orgs_data = []
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	425 for org in ti.organism.get_organisms():
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	426 clean_name = '%s %s' % (org['genus'], org['species'])
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	427 if org['infraspecific_name']:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	428 clean_name += ' (%s)' % (org['infraspecific_name'])
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	429 orgs_data.append((clean_name, org['organism_id'], False))
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	430 return orgs_data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	431
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	432
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	433 def list_analyses(args, *kwargs):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	434
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	435 ti = _get_instance()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	436
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	437 # Key for cached data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	438 cacheKey = 'analyses'
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	439 # We don't want to trust "if key in cache" because between asking and fetch
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	440 # it might through key error.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	441 if cacheKey not in cache:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	442 # However if it ISN'T there, we know we're safe to fetch + put in
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	443 # there.<?xml version="1.0"?>
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	444
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	445 data = _list_analyses(ti, args, *kwargs)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	446 cache[cacheKey] = data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	447 return data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	448 try:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	449 # The cache key may or may not be in the cache at this point, it
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	450 # /likely/ is. However we take no chances that it wasn't evicted between
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	451 # when we checked above and now, so we reference the object from the
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	452 # cache in preparation to return.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	453 data = cache[cacheKey]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	454 return data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	455 except KeyError:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	456 # If access fails due to eviction, we will fail over and can ensure that
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	457 # data is inserted.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	458 data = _list_analyses(ti, args, *kwargs)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	459 cache[cacheKey] = data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	460 return data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	461
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	462
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	463 def _list_analyses(ti, args, *kwargs):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	464 ans_data = []
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	465 for an in ti.analysis.get_analyses():
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	466 ans_data.append((an['name'], an['analysis_id'], False))
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	467 return ans_data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	468
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	469
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	470 def list_blastdbs(args, *kwargs):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	471
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	472 ti = _get_instance()
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	473
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	474 # Key for cached data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	475 cacheKey = 'blastdbs'
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	476 # We don't want to trust "if key in cache" because between asking and fetch
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	477 # it might through key error.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	478 if cacheKey not in cache:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	479 # However if it ISN'T there, we know we're safe to fetch + put in
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	480 # there.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	481 data = _list_blastdbs(ti, args, *kwargs)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	482 cache[cacheKey] = data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	483 return data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	484 try:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	485 # The cache key may or may not be in the cache at this point, it
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	486 # /likely/ is. However we take no chances that it wasn't evicted between
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	487 # when we checked above and now, so we reference the object from the
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	488 # cache in preparation to return.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	489 data = cache[cacheKey]
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	490 return data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	491 except KeyError:
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	492 # If access fails due to eviction, we will fail over and can ensure that
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	493 # data is inserted.
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	494 data = _list_blastdbs(ti, args, *kwargs)
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	495 cache[cacheKey] = data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	496 return data
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	497
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	498
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	499 def _list_blastdbs(ti, args, *kwargs):
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	500 dbs_data = []
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	501 for db in ti.db.get_dbs():
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	502 dbs_data.append((db['name'], db['db_id'], False))
e1d4fad18572 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	503 return dbs_data

Mercurial > repos > gga > tripal_analysis_load_blast

annotate tripal.py @ 0:e1d4fad18572 draft