def __init__(self, autoGC=True, dbname='generic', **kwargs):
"Initialize seq db from filepath or ifile"
if autoGC: # automatically garbage collect unused objects
self._weakValueDict = classutil.RecentValueDictionary(autoGC)
else:
self._weakValueDict = {} # object cache
self.autoGC = autoGC
kwargs = kwargs.copy() # get a copy we can modify w/o side effects
classutil.apply_itemclass(self, kwargs)
kwargs['db'] = self
classutil.get_bound_subclass(self, 'itemClass', dbname,
subclassArgs=kwargs)
self.set_seqtype()
def __init__(self,
filename,
mode=None,
writeback=False,
unpicklingMode=False,
verbose=True,
**kwargs):
'''Wrapper for a shelve object that can be pickled. Ideally, you
should specify a TWO letter mode string: the first letter to
indicate what mode the shelve should be initially opened in, and
the second to indicate the mode to open the shelve during unpickling.
e.g. mode='nr': to create an empty shelve (writable),
which in future will be re-opened read-only.
Also, mode=None makes it first attempt to open read-only, but if the file
does not exist will create it using mode 'c'. '''
# Mark this string as a file path.
self.filename = classutil.SourceFileName(str(filename))
self.writeback = writeback
if unpicklingMode or mode is None or mode == 'r':
# Just use mode as given.
self.mode = mode
elif mode == 'n' or mode == 'c' or mode == 'w':
# Ambiguous modes, warn & set default.
if verbose:
import sys
print >> sys.stderr, '''Warning: you opened shelve file %s
in mode '%s' but this is ambiguous for how the shelve should be
re-opened later during unpickling. By default it will be
re-opened in mode 'r' (read-only). To make it be re-opened
writable, create it in mode '%sw', or call its method
reopen('w'), which will make it be re-opened in mode 'w' now and
in later unpickling. To suppress this warning message, use the
verbose=False option.''' % (filename, mode, mode)
self.mode = 'r'
else: # PROCESS UNAMBIGUOUS TWO-LETTER mode STRING
try:
if len(mode) == 2 and mode[0] in 'ncwr' and mode[1] in 'cwr':
self.mode = mode[1] # IN FUTURE OPEN IN THIS MODE
mode = mode[0] # OPEN NOW IN THIS MODE
else:
raise ValueError('invalid mode string: ' + mode)
except TypeError:
raise ValueError('file mode must be a string!')
if unpicklingMode:
self.d = classutil.open_shelve(filename,
mode,
writeback,
allowReadOnly=True)
else:
self.d = classutil.open_shelve(filename, mode, writeback)
classutil.apply_itemclass(self, kwargs)
def __init__(self, autoGC=True, dbname='generic', **kwargs):
"Initialize seq db from filepath or ifile"
if autoGC: # automatically garbage collect unused objects
self._weakValueDict = classutil.RecentValueDictionary(autoGC)
else:
self._weakValueDict = {} # object cache
self.autoGC = autoGC
kwargs = kwargs.copy() # get a copy we can modify w/o side effects
classutil.apply_itemclass(self, kwargs)
kwargs['db'] = self
classutil.get_bound_subclass(self,
'itemClass',
dbname,
subclassArgs=kwargs)
self.set_seqtype()
def __init__(self, filename, mode=None, writeback=False,
unpicklingMode=False, verbose=True, **kwargs):
'''Wrapper for a shelve object that can be pickled. Ideally, you
should specify a TWO letter mode string: the first letter to
indicate what mode the shelve should be initially opened in, and
the second to indicate the mode to open the shelve during unpickling.
e.g. mode='nr': to create an empty shelve (writable),
which in future will be re-opened read-only.
Also, mode=None makes it first attempt to open read-only, but if the file
does not exist will create it using mode 'c'. '''
# Mark this string as a file path.
self.filename = classutil.SourceFileName(str(filename))
self.writeback = writeback
if unpicklingMode or mode is None or mode == 'r':
# Just use mode as given.
self.mode = mode
elif mode == 'n' or mode == 'c' or mode == 'w':
# Ambiguous modes, warn & set default.
if verbose:
import sys
print >>sys.stderr, '''Warning: you opened shelve file %s
in mode '%s' but this is ambiguous for how the shelve should be
re-opened later during unpickling. By default it will be
re-opened in mode 'r' (read-only). To make it be re-opened
writable, create it in mode '%sw', or call its method
reopen('w'), which will make it be re-opened in mode 'w' now and
in later unpickling. To suppress this warning message, use the
verbose=False option.''' % (filename, mode, mode)
self.mode = 'r'
else: # PROCESS UNAMBIGUOUS TWO-LETTER mode STRING
try:
if len(mode) == 2 and mode[0] in 'ncwr' and mode[1] in 'cwr':
self.mode = mode[1] # IN FUTURE OPEN IN THIS MODE
mode = mode[0] # OPEN NOW IN THIS MODE
else:
raise ValueError('invalid mode string: ' + mode)
except TypeError:
raise ValueError('file mode must be a string!')
if unpicklingMode:
self.d = classutil.open_shelve(filename, mode, writeback,
allowReadOnly=True)
else:
self.d = classutil.open_shelve(filename, mode, writeback)
classutil.apply_itemclass(self, kwargs)
def __init__(self,saveDict=None,dictClass=dict,**kwargs):
'''saveDict, if not None, is the internal mapping to use as our storage.
filename: if provided, is a file path to a shelve (BerkeleyDB) file to
store the data in.
dictClass: if provided, is the class to use for storage of the dict data.'''
if saveDict is not None:
self.d = saveDict
elif 'filename' in kwargs: # USE A SHELVE (BERKELEY DB)
try:
if kwargs['intKeys']: # ALLOW INT KEYS, HAVE TO USE IntShelve
self.__class__ = IntShelve
else:
raise KeyError
except KeyError:
self.__class__ = PicklableShelve
return self.__init__(**kwargs)
else:
self.d = dictClass()
classutil.apply_itemclass(self,kwargs)
def __init__(self, saveDict=None, dictClass=dict, **kwargs):
'''saveDict, if not None, the internal mapping to use as our storage.
filename: if provided, a file path to a shelve (BerkeleyDB) file to
store the data in.
dictClass: if provided, the class to use for storage of dict data.'''
if saveDict is not None:
self.d = saveDict
elif 'filename' in kwargs: # USE A SHELVE (BERKELEY DB)
try:
if kwargs['intKeys']: # ALLOW INT KEYS, HAVE TO USE IntShelve
self.__class__ = IntShelve
else:
raise KeyError
except KeyError:
self.__class__ = PicklableShelve
return self.__init__(**kwargs)
else:
self.d = dictClass()
classutil.apply_itemclass(self, kwargs)