apollo_delete_organism: webapollo.py annotate

annotate webapollo.py @ 17:8f4c1d40e893 draft default tip

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b

author	gga
date	Wed, 11 Jan 2023 11:48:59 +0000
parents	dd63c6e11a95
children

rev	line source
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	1 from __future__ import print_function
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	2
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	3 import argparse
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	4 import collections
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	5 import json
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	6 import logging
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	7 import os
17 8f4c1d40e893 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b gga parents: 10 diff changeset	8 import sys
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	9 import time
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	10 from abc import abstractmethod
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	11
17 8f4c1d40e893 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b gga parents: 10 diff changeset	12 if sys.version_info.major == 3 and sys.version_info.minor >= 10:
8f4c1d40e893 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b gga parents: 10 diff changeset	13 from collections.abc import MutableMapping
8f4c1d40e893 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b gga parents: 10 diff changeset	14 else:
8f4c1d40e893 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b gga parents: 10 diff changeset	15 from collections import MutableMapping
8f4c1d40e893 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b gga parents: 10 diff changeset	16
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	17 import requests
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	18
4 a5de2095bd01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e gga parents: 2 diff changeset	19 from six.moves.builtins import next
a5de2095bd01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e gga parents: 2 diff changeset	20 from six.moves.builtins import object
a5de2095bd01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e gga parents: 2 diff changeset	21
10 dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	22 import yaml
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	23
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	24 logging.getLogger("requests").setLevel(logging.CRITICAL)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	25 log = logging.getLogger()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	26
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	27
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	28 #############################################
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	29 # BEGIN IMPORT OF CACHING LIBRARY #
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	30 #############################################
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	31 # This code is licensed under the MIT #
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	32 # License and is a copy of code publicly #
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	33 # available in rev. #
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	34 # e27332bc82f4e327aedaec17c9b656ae719322ed #
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	35 # of https://github.com/tkem/cachetools/ #
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	36 #############################################
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	37
17 8f4c1d40e893 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b gga parents: 10 diff changeset	38 class DefaultMapping(MutableMapping):
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	39
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	40 __slots__ = ()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	41
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	42 @abstractmethod
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	43 def __contains__(self, key): # pragma: nocover
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	44 return False
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	45
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	46 @abstractmethod
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	47 def __getitem__(self, key): # pragma: nocover
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	48 if hasattr(self.__class__, '__missing__'):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	49 return self.__class__.__missing__(self, key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	50 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	51 raise KeyError(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	52
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	53 def get(self, key, default=None):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	54 if key in self:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	55 return self[key]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	56 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	57 return default
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	58
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	59 __marker = object()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	60
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	61 def pop(self, key, default=__marker):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	62 if key in self:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	63 value = self[key]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	64 del self[key]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	65 elif default is self.__marker:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	66 raise KeyError(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	67 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	68 value = default
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	69 return value
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	70
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	71 def setdefault(self, key, default=None):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	72 if key in self:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	73 value = self[key]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	74 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	75 self[key] = value = default
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	76 return value
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	77
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	78
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	79 DefaultMapping.register(dict)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	80
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	81
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	82 class _DefaultSize(object):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	83 def __getitem__(self, _):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	84 return 1
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	85
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	86 def __setitem__(self, _, value):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	87 assert value == 1
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	88
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	89 def pop(self, _):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	90 return 1
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	91
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	92
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	93 class Cache(DefaultMapping):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	94 """Mutable mapping to serve as a simple cache or cache base class."""
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	95
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	96 __size = _DefaultSize()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	97
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	98 def __init__(self, maxsize, missing=None, getsizeof=None):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	99 if missing:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	100 self.__missing = missing
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	101 if getsizeof:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	102 self.__getsizeof = getsizeof
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	103 self.__size = dict()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	104 self.__data = dict()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	105 self.__currsize = 0
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	106 self.__maxsize = maxsize
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	107
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	108 def __repr__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	109 return '%s(%r, maxsize=%r, currsize=%r)' % (
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	110 self.__class__.__name__,
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	111 list(self.__data.items()),
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	112 self.__maxsize,
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	113 self.__currsize,
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	114 )
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	115
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	116 def __getitem__(self, key):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	117 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	118 return self.__data[key]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	119 except KeyError:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	120 return self.__missing__(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	121
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	122 def __setitem__(self, key, value):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	123 maxsize = self.__maxsize
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	124 size = self.getsizeof(value)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	125 if size > maxsize:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	126 raise ValueError('value too large')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	127 if key not in self.__data or self.__size[key] < size:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	128 while self.__currsize + size > maxsize:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	129 self.popitem()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	130 if key in self.__data:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	131 diffsize = size - self.__size[key]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	132 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	133 diffsize = size
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	134 self.__data[key] = value
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	135 self.__size[key] = size
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	136 self.__currsize += diffsize
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	137
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	138 def __delitem__(self, key):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	139 size = self.__size.pop(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	140 del self.__data[key]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	141 self.__currsize -= size
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	142
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	143 def __contains__(self, key):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	144 return key in self.__data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	145
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	146 def __missing__(self, key):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	147 value = self.__missing(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	148 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	149 self.__setitem__(key, value)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	150 except ValueError:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	151 pass # value too large
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	152 return value
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	153
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	154 def __iter__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	155 return iter(self.__data)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	156
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	157 def __len__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	158 return len(self.__data)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	159
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	160 @staticmethod
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	161 def __getsizeof(value):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	162 return 1
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	163
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	164 @staticmethod
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	165 def __missing(key):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	166 raise KeyError(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	167
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	168 @property
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	169 def maxsize(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	170 """The maximum size of the cache."""
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	171 return self.__maxsize
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	172
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	173 @property
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	174 def currsize(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	175 """The current size of the cache."""
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	176 return self.__currsize
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	177
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	178 def getsizeof(self, value):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	179 """Return the size of a cache element's value."""
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	180 return self.__getsizeof(value)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	181
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	182
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	183 class _Link(object):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	184
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	185 __slots__ = ('key', 'expire', 'next', 'prev')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	186
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	187 def __init__(self, key=None, expire=None):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	188 self.key = key
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	189 self.expire = expire
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	190
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	191 def __reduce__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	192 return _Link, (self.key, self.expire)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	193
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	194 def unlink(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	195 next = self.next
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	196 prev = self.prev
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	197 prev.next = next
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	198 next.prev = prev
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	199
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	200
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	201 class _Timer(object):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	202
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	203 def __init__(self, timer):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	204 self.__timer = timer
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	205 self.__nesting = 0
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	206
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	207 def __call__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	208 if self.__nesting == 0:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	209 return self.__timer()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	210 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	211 return self.__time
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	212
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	213 def __enter__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	214 if self.__nesting == 0:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	215 self.__time = time = self.__timer()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	216 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	217 time = self.__time
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	218 self.__nesting += 1
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	219 return time
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	220
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	221 def __exit__(self, *exc):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	222 self.__nesting -= 1
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	223
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	224 def __reduce__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	225 return _Timer, (self.__timer,)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	226
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	227 def __getattr__(self, name):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	228 return getattr(self.__timer, name)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	229
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	230
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	231 class TTLCache(Cache):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	232 """LRU Cache implementation with per-item time-to-live (TTL) value."""
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	233
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	234 def __init__(self, maxsize, ttl, timer=time.time, missing=None,
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	235 getsizeof=None):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	236 Cache.__init__(self, maxsize, missing, getsizeof)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	237 self.__root = root = _Link()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	238 root.prev = root.next = root
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	239 self.__links = collections.OrderedDict()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	240 self.__timer = _Timer(timer)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	241 self.__ttl = ttl
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	242
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	243 def __contains__(self, key):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	244 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	245 link = self.__links[key] # no reordering
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	246 except KeyError:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	247 return False
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	248 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	249 return not (link.expire < self.__timer())
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	250
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	251 def __getitem__(self, key, cache_getitem=Cache.__getitem__):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	252 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	253 link = self.__getlink(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	254 except KeyError:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	255 expired = False
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	256 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	257 expired = link.expire < self.__timer()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	258 if expired:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	259 return self.__missing__(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	260 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	261 return cache_getitem(self, key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	262
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	263 def __setitem__(self, key, value, cache_setitem=Cache.__setitem__):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	264 with self.__timer as time:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	265 self.expire(time)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	266 cache_setitem(self, key, value)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	267 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	268 link = self.__getlink(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	269 except KeyError:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	270 self.__links[key] = link = _Link(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	271 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	272 link.unlink()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	273 link.expire = time + self.__ttl
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	274 link.next = root = self.__root
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	275 link.prev = prev = root.prev
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	276 prev.next = root.prev = link
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	277
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	278 def __delitem__(self, key, cache_delitem=Cache.__delitem__):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	279 cache_delitem(self, key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	280 link = self.__links.pop(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	281 link.unlink()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	282 if link.expire < self.__timer():
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	283 raise KeyError(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	284
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	285 def __iter__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	286 root = self.__root
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	287 curr = root.next
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	288 while curr is not root:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	289 # "freeze" time for iterator access
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	290 with self.__timer as time:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	291 if not (curr.expire < time):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	292 yield curr.key
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	293 curr = curr.next
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	294
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	295 def __len__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	296 root = self.__root
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	297 curr = root.next
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	298 time = self.__timer()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	299 count = len(self.__links)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	300 while curr is not root and curr.expire < time:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	301 count -= 1
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	302 curr = curr.next
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	303 return count
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	304
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	305 def __setstate__(self, state):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	306 self.__dict__.update(state)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	307 root = self.__root
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	308 root.prev = root.next = root
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	309 for link in sorted(self.__links.values(), key=lambda obj: obj.expire):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	310 link.next = root
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	311 link.prev = prev = root.prev
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	312 prev.next = root.prev = link
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	313 self.expire(self.__timer())
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	314
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	315 def __repr__(self, cache_repr=Cache.__repr__):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	316 with self.__timer as time:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	317 self.expire(time)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	318 return cache_repr(self)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	319
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	320 @property
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	321 def currsize(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	322 with self.__timer as time:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	323 self.expire(time)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	324 return super(TTLCache, self).currsize
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	325
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	326 @property
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	327 def timer(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	328 """The timer function used by the cache."""
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	329 return self.__timer
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	330
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	331 @property
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	332 def ttl(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	333 """The time-to-live value of the cache's items."""
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	334 return self.__ttl
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	335
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	336 def expire(self, time=None):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	337 """Remove expired items from the cache."""
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	338 if time is None:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	339 time = self.__timer()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	340 root = self.__root
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	341 curr = root.next
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	342 links = self.__links
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	343 cache_delitem = Cache.__delitem__
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	344 while curr is not root and curr.expire < time:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	345 cache_delitem(self, curr.key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	346 del links[curr.key]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	347 next = curr.next
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	348 curr.unlink()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	349 curr = next
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	350
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	351 def clear(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	352 with self.__timer as time:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	353 self.expire(time)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	354 Cache.clear(self)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	355
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	356 def get(self, args, *kwargs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	357 with self.__timer:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	358 return Cache.get(self, args, *kwargs)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	359
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	360 def pop(self, args, *kwargs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	361 with self.__timer:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	362 return Cache.pop(self, args, *kwargs)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	363
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	364 def setdefault(self, args, *kwargs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	365 with self.__timer:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	366 return Cache.setdefault(self, args, *kwargs)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	367
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	368 def popitem(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	369 """Remove and return the `(key, value)` pair least recently used that
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	370 has not already expired.
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	371
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	372 """
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	373 with self.__timer as time:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	374 self.expire(time)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	375 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	376 key = next(iter(self.__links))
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	377 except StopIteration:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	378 raise KeyError('%s is empty' % self.__class__.__name__)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	379 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	380 return (key, self.pop(key))
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	381
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	382 if hasattr(collections.OrderedDict, 'move_to_end'):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	383 def __getlink(self, key):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	384 value = self.__links[key]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	385 self.__links.move_to_end(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	386 return value
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	387 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	388 def __getlink(self, key):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	389 value = self.__links.pop(key)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	390 self.__links[key] = value
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	391 return value
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	392
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	393
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	394 #############################################
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	395 # END IMPORT OF CACHING LIBRARY #
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	396 #############################################
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	397
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	398
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	399 cache = TTLCache(
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	400 100, # Up to 100 items
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	401 5 * 60 # 5 minute cache life
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	402 )
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	403 userCache = TTLCache(
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	404 2, # Up to 2 items
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	405 60 # 1 minute cache life
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	406 )
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	407
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	408
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	409 class UnknownUserException(Exception):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	410 pass
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	411
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	412
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	413 def WAAuth(parser):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	414 parser.add_argument('apollo', help='Complete Apollo URL')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	415 parser.add_argument('username', help='WA Username')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	416 parser.add_argument('password', help='WA Password')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	417
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	418
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	419 def OrgOrGuess(parser):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	420 parser.add_argument('--org_json', type=argparse.FileType("r"), help='Apollo JSON output, source for common name')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	421 parser.add_argument('--org_raw', help='Common Name')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	422 parser.add_argument('--org_id', help='Organism ID')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	423
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	424
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	425 def CnOrGuess(parser):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	426 OrgOrGuess(parser)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	427 parser.add_argument('--seq_fasta', type=argparse.FileType("r"), help='Fasta file, IDs used as sequence sources')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	428 parser.add_argument('--seq_raw', nargs='*', help='Sequence Names')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	429
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	430
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	431 def AssertUser(user_list):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	432 if len(user_list) == 0:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	433 raise UnknownUserException()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	434 elif len(user_list) == 1:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	435 return user_list[0]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	436 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	437 raise Exception("Too many users!")
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	438
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	439
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	440 class WebApolloInstance(object):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	441
10 dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	442 def __init__(self):
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	443
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	444 if 'ARROW_GLOBAL_CONFIG_PATH' in os.environ:
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	445 with open(os.environ['ARROW_GLOBAL_CONFIG_PATH'], 'r') as config:
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	446 conf = yaml.safe_load(config)
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	447 try:
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	448 instance_name = conf['__default']
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	449 except KeyError:
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	450 raise Exception("Unknown Apollo instance and no __default provided")
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	451 self.apollo_url = conf[instance_name]['url']
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	452 self.username = conf[instance_name]['username']
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	453 self.password = conf[instance_name]['password']
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	454 else:
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	455 self.apollo_url = os.environ['GALAXY_WEBAPOLLO_URL']
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	456 self.username = os.environ['GALAXY_WEBAPOLLO_USER']
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	457 self.password = os.environ['GALAXY_WEBAPOLLO_PASSWORD']
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	458
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	459 self.groups = GroupsClient(self)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	460 self.organisms = OrganismsClient(self)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	461 self.users = UsersClient(self)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	462
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	463 def __str__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	464 return '<WebApolloInstance at %s>' % self.apollo_url
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	465
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	466 def requireUser(self, email):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	467 cacheKey = 'user-list'
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	468 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	469 # Get the cached value
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	470 data = userCache[cacheKey]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	471 except KeyError:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	472 # If we hit a key error above, indicating that
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	473 # we couldn't find the key, we'll simply re-request
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	474 # the data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	475 data = self.users.loadUsers()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	476 userCache[cacheKey] = data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	477
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	478 return AssertUser([x for x in data if x.username == email])
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	479
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	480
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	481 class GroupObj(object):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	482 def __init__(self, **kwargs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	483 self.name = kwargs['name']
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	484
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	485 if 'id' in kwargs:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	486 self.groupId = kwargs['id']
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	487
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	488
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	489 class UserObj(object):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	490 ROLE_USER = 'USER'
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	491 ROLE_ADMIN = 'ADMIN'
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	492
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	493 def __init__(self, **kwargs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	494 # Generally expect 'userId', 'firstName', 'lastName', 'username' (email)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	495 for attr in kwargs.keys():
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	496 setattr(self, attr, kwargs[attr])
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	497
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	498 if 'groups' in kwargs:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	499 groups = []
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	500 for groupData in kwargs['groups']:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	501 groups.append(GroupObj(**groupData))
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	502 self.groups = groups
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	503
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	504 self.__props = kwargs.keys()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	505
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	506 def __str__(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	507 return '<User %s: %s %s <%s>>' % (self.userId, self.firstName,
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	508 self.lastName, self.username)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	509
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	510
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	511 class Client(object):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	512
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	513 def __init__(self, webapolloinstance, **requestArgs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	514 self._wa = webapolloinstance
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	515
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	516 self.__verify = requestArgs.get('verify', True)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	517 self._requestArgs = requestArgs
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	518
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	519 if 'verify' in self._requestArgs:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	520 del self._requestArgs['verify']
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	521
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	522 def request(self, clientMethod, data, post_params={}, isJson=True):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	523 url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	524
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	525 headers = {
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	526 'Content-Type': 'application/json'
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	527 }
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	528
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	529 data.update({
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	530 'username': self._wa.username,
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	531 'password': self._wa.password,
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	532 })
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	533
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	534 r = requests.post(url, data=json.dumps(data), headers=headers,
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	535 verify=self.__verify, params=post_params, allow_redirects=False, **self._requestArgs)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	536
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	537 if r.status_code == 200 or r.status_code == 302:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	538 if isJson:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	539 d = r.json()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	540 if 'username' in d:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	541 del d['username']
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	542 if 'password' in d:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	543 del d['password']
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	544 return d
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	545 else:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	546 return r.text
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	547
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	548 # @see self.body for HTTP response body
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	549 raise Exception("Unexpected response from apollo %s: %s" %
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	550 (r.status_code, r.text))
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	551
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	552 def get(self, clientMethod, get_params):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	553 url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	554 headers = {}
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	555
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	556 r = requests.get(url, headers=headers, verify=self.__verify,
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	557 params=get_params, **self._requestArgs)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	558 if r.status_code == 200:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	559 d = r.json()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	560 if 'username' in d:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	561 del d['username']
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	562 if 'password' in d:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	563 del d['password']
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	564 return d
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	565 # @see self.body for HTTP response body
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	566 raise Exception("Unexpected response from apollo %s: %s" %
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	567 (r.status_code, r.text))
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	568
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	569
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	570 class GroupsClient(Client):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	571 CLIENT_BASE = '/group/'
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	572
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	573 def loadGroups(self, group=None):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	574 res = self.request('loadGroups', {})
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	575 data = [GroupObj(**x) for x in res]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	576 if group is not None:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	577 data = [x for x in data if x.name == group]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	578
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	579 return data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	580
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	581
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	582 class OrganismsClient(Client):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	583 CLIENT_BASE = '/organism/'
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	584
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	585 def findAllOrganisms(self):
5 0af4179e6758 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2 gga parents: 4 diff changeset	586 orgs = self.request('findAllOrganisms', {})
0af4179e6758 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2 gga parents: 4 diff changeset	587 if not isinstance(orgs, (list,)):
0af4179e6758 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2 gga parents: 4 diff changeset	588 orgs = []
0af4179e6758 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2 gga parents: 4 diff changeset	589 return orgs
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	590
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	591
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	592 class UsersClient(Client):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	593 CLIENT_BASE = '/user/'
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	594
10 dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	595 def loadUsers(self):
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	596 res = self.request('loadUsers', {})
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	597
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	598 data = [UserObj(**x) for x in res]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	599
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	600 return data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	601
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	602
10 dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	603 def handle_credentials(user):
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	604 if hasattr(user, 'new_password'):
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	605 f = open("Apollo_credentials.txt", "w")
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	606 f.write('Username:\t%s\nPassword:\t%s' % (user.username, user.new_password))
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	607
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	608
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	609 def accessible_organisms(user, orgs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	610 permissionMap = {
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	611 x['organism']: x['permissions']
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	612 for x in user.organismPermissions
6 db98cd19587b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit d9f27b297d9a919471c92b02ecf6cc9554457211 gga parents: 5 diff changeset	613 if 'WRITE' in x['permissions'] or 'READ' in x['permissions'] or 'ADMINISTRATE' in x['permissions'] or user.role == 'ADMIN'
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	614 }
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	615
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	616 if 'error' in orgs:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	617 raise Exception("Error received from Apollo server: \"%s\"" % orgs['error'])
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	618
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	619 return [
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	620 (org['commonName'], org['id'], False)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	621 for org in sorted(orgs, key=lambda x: x['commonName'])
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	622 if org['commonName'] in permissionMap
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	623 ]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	624
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	625
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	626 def galaxy_list_groups(trans, args, *kwargs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	627 email = trans.get_user().email
10 dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	628 wa = WebApolloInstance()
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	629
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	630 # Key for cached data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	631 cacheKey = 'groups-' + email
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	632 # We don't want to trust "if key in cache" because between asking and fetch
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	633 # it might through key error.
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	634 if cacheKey not in cache:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	635 # However if it ISN'T there, we know we're safe to fetch + put in
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	636 # there.
5 0af4179e6758 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2 gga parents: 4 diff changeset	637 data = _galaxy_list_groups(wa, args, *kwargs)
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	638 cache[cacheKey] = data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	639 return data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	640 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	641 # The cache key may or may not be in the cache at this point, it
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	642 # /likely/ is. However we take no chances that it wasn't evicted between
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	643 # when we checked above and now, so we reference the object from the
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	644 # cache in preparation to return.
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	645 data = cache[cacheKey]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	646 return data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	647 except KeyError:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	648 # If access fails due to eviction, we will fail over and can ensure that
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	649 # data is inserted.
5 0af4179e6758 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2 gga parents: 4 diff changeset	650 data = _galaxy_list_groups(wa, args, *kwargs)
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	651 cache[cacheKey] = data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	652 return data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	653
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	654
5 0af4179e6758 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2 gga parents: 4 diff changeset	655 def _galaxy_list_groups(wa, args, *kwargs):
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	656 # Fetch the groups.
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	657 group_data = []
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	658 for group in wa.groups.loadGroups():
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	659 # Reformat
2 720f372226eb planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 33ce5bd0cce35a12725b9ef9aed0683f3c41fbf9 gga parents: 0 diff changeset	660 group_data.append((group.name, group.name, False))
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	661 return group_data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	662
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	663
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	664 def galaxy_list_orgs(trans, args, *kwargs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	665 email = trans.get_user().email
10 dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	666 wa = WebApolloInstance()
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	667 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	668 gx_user = wa.requireUser(email)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	669 except UnknownUserException:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	670 return []
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	671
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	672 # Key for cached data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	673 cacheKey = 'orgs-' + email
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	674 if cacheKey not in cache:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	675 data = _galaxy_list_orgs(wa, gx_user, args, *kwargs)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	676 cache[cacheKey] = data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	677 return data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	678 try:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	679 data = cache[cacheKey]
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	680 return data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	681 except KeyError:
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	682 data = _galaxy_list_orgs(wa, gx_user, args, *kwargs)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	683 cache[cacheKey] = data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	684 return data
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	685
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	686
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	687 def _galaxy_list_orgs(wa, gx_user, args, *kwargs):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	688 # Fetch all organisms
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	689 all_orgs = wa.organisms.findAllOrganisms()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	690 # Figure out which are accessible to the user
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	691 orgs = accessible_organisms(gx_user, all_orgs)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	692 # Return org list
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	693 return orgs
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	694
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	695
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	696 # This is all for implementing the command line interface for testing.
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	697 class obj(object):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	698 pass
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	699
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	700
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	701 class fakeTrans(object):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	702
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	703 def __init__(self, username):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	704 self.un = username
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	705
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	706 def get_user(self):
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	707 o = obj()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	708 o.email = self.un
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	709 return o
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	710
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	711
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	712 if __name__ == '__main__':
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	713 parser = argparse.ArgumentParser(description='Test access to apollo server')
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	714 parser.add_argument('email', help='Email of user to test')
10 dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	715 parser.add_argument('--action', choices=['org', 'group'], default='org', help='Data set to test, fetch a list of groups or orgs known to the requesting user.')
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	716 args = parser.parse_args()
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	717
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	718 trans = fakeTrans(args.email)
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	719 if args.action == 'org':
10 dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	720 print(galaxy_list_orgs(trans))
0 dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268 gga parents: diff changeset	721 elif args.action == 'group':
10 dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" gga parents: 6 diff changeset	722 print(galaxy_list_groups(trans))

Mercurial > repos > gga > apollo_delete_organism

annotate webapollo.py @ 17:8f4c1d40e893 draft default tip