def test_config_and_collector_pickling(self, testdir):
from cPickle import Pickler, Unpickler
tmpdir = testdir.tmpdir
dir1 = tmpdir.ensure("somedir", dir=1)
config = testdir.parseconfig()
col = config.getfsnode(config.topdir)
col1 = col.join(dir1.basename)
assert col1.parent is col
io = py.std.cStringIO.StringIO()
pickler = Pickler(io)
pickler.dump(col)
pickler.dump(col1)
pickler.dump(col)
io.seek(0)
unpickler = Unpickler(io)
topdir = tmpdir.ensure("newtopdir", dir=1)
topdir.ensure("somedir", dir=1)
old = topdir.chdir()
try:
newcol = unpickler.load()
newcol2 = unpickler.load()
newcol3 = unpickler.load()
assert newcol2.config is newcol.config
assert newcol2.parent == newcol
assert newcol2.config.topdir.realpath() == topdir.realpath()
assert newcol.fspath.realpath() == topdir.realpath()
assert newcol2.fspath.basename == dir1.basename
assert newcol2.fspath.relto(newcol2.config.topdir)
finally:
old.chdir()
def zodb_unpickle(data):
"""Unpickle an object stored using the format expected by ZODB."""
f = StringIO(data)
u = Unpickler(f)
u.persistent_load = persistent_load
klass_info = u.load()
if isinstance(klass_info, types.TupleType):
if isinstance(klass_info[0], type):
# Unclear: what is the second part of klass_info?
klass, xxx = klass_info
assert not xxx
else:
if isinstance(klass_info[0], tuple):
modname, klassname = klass_info[0]
else:
modname, klassname = klass_info
if modname == "__main__":
ns = globals()
else:
mod = import_helper(modname)
ns = mod.__dict__
try:
klass = ns[klassname]
except KeyError:
print >> sys.stderr, "can't find %s in %r" % (klassname, ns)
inst = klass()
else:
raise ValueError("expected class info: %s" % repr(klass_info))
state = u.load()
inst.__setstate__(state)
return inst
def load_weights(self):
''' Loads the stored data from previous sessions, if possible.'''
valid = False
try: fp = open(self.filename, 'r')
except IOError:
self.log_debug(11, "Couldn't read stats file '%s'", self.filename)
else:
self.log_debug(11, "Loading stats file '%s'", self.filename)
try:
pickler = Unpickler(fp)
self.input_headers = pickler.load()
wi = pickler.load()
self.output_headers = pickler.load()
wo = pickler.load()
#self.seasons = pickler.load()
#self.powers = pickler.load()
#self.locs = pickler.load()
#self.provinces = pickler.load()
#self.centers = pickler.load()
#self.coastals = pickler.load()
#self.coastlines = pickler.load()
#self.borders = pickler.load()
finally:
fp.close()
ni = len(self.input_headers)
no = len(self.output_headers)
nh = len(wo)
self.log_debug(7, "%d inputs => %d hidden => %d outputs",
ni, nh, no)
self.net = NN(ni, nh, no, wi, wo)
valid = True
return valid
def setstate(self, object):
"""
Unlike the 'stock' Connection class' setstate, this method
doesn't raise ConflictErrors. This is potentially dangerous
for applications that need absolute consistency, but
sessioning is not one of those.
"""
oid = object._p_oid
invalid = self._invalid
if invalid(None):
# only raise a conflict if there was
# a mass invalidation, but not if we see this
# object's oid as invalid
raise ConflictError, ` oid `
p, serial = self._storage.load(oid, self._version)
file = StringIO(p)
unpickler = Unpickler(file)
unpickler.persistent_load = self._persistent_load
unpickler.load()
state = unpickler.load()
if hasattr(object, '__setstate__'):
object.__setstate__(state)
else:
d = object.__dict__
for k, v in state.items():
d[k] = v
object._p_serial = serial
def test_config_and_collector_pickling(self):
from cPickle import Pickler, Unpickler
dir1 = self.tmpdir.ensure("somedir", dir=1)
config = py.test.config._reparse([self.tmpdir])
col = config.getfsnode(config.topdir)
col1 = col.join(dir1.basename)
assert col1.parent is col
io = py.std.cStringIO.StringIO()
pickler = Pickler(io)
pickler.dump(config)
pickler.dump(col)
pickler.dump(col1)
pickler.dump(col)
io.seek(0)
unpickler = Unpickler(io)
newconfig = unpickler.load()
topdir = self.tmpdir.ensure("newtopdir", dir=1)
newconfig._initafterpickle(topdir)
topdir.ensure("somedir", dir=1)
newcol = unpickler.load()
newcol2 = unpickler.load()
newcol3 = unpickler.load()
assert newcol2._config is newconfig
assert newcol2.parent == newcol
assert newcol._config is newconfig
assert newconfig.topdir == topdir
assert newcol3 is newcol
assert newcol.fspath == topdir
assert newcol2.fspath.basename == dir1.basename
assert newcol2.fspath.relto(topdir)
def tryToResolveConflict(self,
oid,
committedSerial,
oldSerial,
newpickle,
committedData=''):
# class_tuple, old, committed, newstate = ('',''), 0, 0, 0
try:
prfactory = PersistentReferenceFactory()
newpickle = self._crs_untransform_record_data(newpickle)
file = StringIO(newpickle)
unpickler = Unpickler(file)
unpickler.find_global = find_global
unpickler.persistent_load = prfactory.persistent_load
meta = unpickler.load()
if isinstance(meta, tuple):
klass = meta[0]
newargs = meta[1] or ()
if isinstance(klass, tuple):
klass = find_global(*klass)
else:
klass = meta
newargs = ()
if klass in _unresolvable:
raise ConflictError
newstate = unpickler.load()
inst = klass.__new__(klass, *newargs)
try:
resolve = inst._p_resolveConflict
except AttributeError:
_unresolvable[klass] = 1
raise ConflictError
old = state(self, oid, oldSerial, prfactory)
committed = state(self, oid, committedSerial, prfactory, committedData)
resolved = resolve(old, committed, newstate)
file = StringIO()
pickler = Pickler(file, 1)
pickler.inst_persistent_id = persistent_id
pickler.dump(meta)
pickler.dump(resolved)
return self._crs_transform_record_data(file.getvalue(1))
except (ConflictError, BadClassName):
pass
except:
# If anything else went wrong, catch it here and avoid passing an
# arbitrary exception back to the client. The error here will mask
# the original ConflictError. A client can recover from a
# ConflictError, but not necessarily from other errors. But log
# the error so that any problems can be fixed.
logger.error("Unexpected error", exc_info=True)
raise ConflictError(oid=oid,
serials=(committedSerial, oldSerial),
data=newpickle)
def load_state(self, state):
"""Load an image_set_list's state from the string returned from save_state"""
self.__image_sets = []
self.__image_sets_by_key = {}
# Make a safe unpickler
p = Unpickler(StringIO(state))
def find_global(module_name, class_name):
logger.debug("Pickler wants %s:%s", module_name, class_name)
if module_name not in ("numpy", "numpy.core.multiarray"):
logger.critical(
"WARNING WARNING WARNING - your batch file has asked to load %s.%s."
" If this looks in any way suspicious please contact us at www.cellprofiler.org",
module_name,
class_name,
)
raise ValueError("Illegal attempt to unpickle class %s.%s", (module_name, class_name))
__import__(module_name)
mod = sys.modules[module_name]
return getattr(mod, class_name)
p.find_global = find_global
count = p.load()
all_keys = [p.load() for i in range(count)]
self.__legacy_fields = p.load()
#
# Have to do in this order in order for the image set's
# legacy_fields property to hook to the right legacy_fields
#
for i in range(count):
self.get_image_set(all_keys[i])
def test_config_and_collector_pickling(self, testdir):
from cPickle import Pickler, Unpickler
tmpdir = testdir.tmpdir
dir1 = tmpdir.ensure("somedir", dir=1)
config = testdir.parseconfig()
col = config.getfsnode(config.topdir)
col1 = col.join(dir1.basename)
assert col1.parent is col
io = py.std.cStringIO.StringIO()
pickler = Pickler(io)
pickler.dump(col)
pickler.dump(col1)
pickler.dump(col)
io.seek(0)
unpickler = Unpickler(io)
topdir = tmpdir.ensure("newtopdir", dir=1)
topdir.ensure("somedir", dir=1)
old = topdir.chdir()
try:
newcol = unpickler.load()
newcol2 = unpickler.load()
newcol3 = unpickler.load()
assert newcol2.config is newcol.config
assert newcol2.parent == newcol
assert newcol2.config.topdir.realpath() == topdir.realpath()
assert newcol.fspath.realpath() == topdir.realpath()
assert newcol2.fspath.basename == dir1.basename
assert newcol2.fspath.relto(newcol2.config.topdir)
finally:
old.chdir()
def __init__(self, inp_filename):
self.filename = inp_filename
with open(self.filename, 'rb') as inpfile:
reader = Unpickler(inpfile)
self.numgroups = reader.load()
self.tot_msgs = reader.load()
self.num_msgs = reader.load()
def __init__(self, inp_filename):
self.filename = inp_filename
with open(self.filename, 'rb') as inpfile:
reader = Unpickler(inpfile)
self.numgroups = reader.load()
self.tot_msgs = reader.load()
self.num_msgs = reader.load()
def deserialize(self, event, state):
assert IFullDeserializationEvent.isImplementedBy(event)
assert isinstance(event.obj, Persistent)
# Set up to resolve cyclic references to the object.
event.deserialized('self', event.obj)
state = state.strip()
if state:
if state.startswith('#'):
# Text-encoded pickles start with a pound sign.
# (A pound sign is not a valid pickle opcode.)
data = decode_from_text(state)
else:
data = state
infile = StringIO(data)
u = Unpickler(infile)
u.persistent_load = event.resolve_internal
s = u.load()
if not hasattr(s, 'items'):
# Turn the list back into a dictionary
s_list = s
s = {}
for key, value in s_list:
s[key] = value
event.obj.__dict__.update(s)
try:
unmanaged = u.load()
except EOFError:
# old pickle with no list of unmanaged objects
pass
else:
event.upos.extend(unmanaged)
def setstate(self, object):
"""
Unlike the 'stock' Connection class' setstate, this method
doesn't raise ConflictErrors. This is potentially dangerous
for applications that need absolute consistency, but
sessioning is not one of those.
"""
oid=object._p_oid
invalid = self._invalid
if invalid(None):
# only raise a conflict if there was
# a mass invalidation, but not if we see this
# object's oid as invalid
raise ConflictError, `oid`
p, serial = self._storage.load(oid, self._version)
file=StringIO(p)
unpickler=Unpickler(file)
unpickler.persistent_load=self._persistent_load
unpickler.load()
state = unpickler.load()
if hasattr(object, '__setstate__'):
object.__setstate__(state)
else:
d=object.__dict__
for k,v in state.items(): d[k]=v
object._p_serial=serial
def zodb_unpickle(data):
"""Unpickle an object stored using the format expected by ZODB."""
f = StringIO(data)
u = Unpickler(f)
u.persistent_load = persistent_load
klass_info = u.load()
if isinstance(klass_info, tuple):
if isinstance(klass_info[0], type):
# Unclear: what is the second part of klass_info?
klass, xxx = klass_info
assert not xxx
else:
if isinstance(klass_info[0], tuple):
modname, klassname = klass_info[0]
else:
modname, klassname = klass_info
if modname == "__main__":
ns = globals()
else:
mod = import_helper(modname)
ns = mod.__dict__
try:
klass = ns[klassname]
except KeyError:
print >> sys.stderr, "can't find %s in %r" % (klassname, ns)
inst = klass()
else:
raise ValueError("expected class info: %s" % repr(klass_info))
state = u.load()
inst.__setstate__(state)
return inst
def zodb_unpickle(data):
"""Unpickle an object stored using the format expected by ZODB."""
f = StringIO(data)
u = Unpickler(f)
klass_info = u.load()
if isinstance(klass_info, types.TupleType):
if isinstance(klass_info[0], types.TupleType):
modname, klassname = klass_info[0]
args = klass_info[1]
else:
modname, klassname = klass_info
args = None
if modname == "__main__":
ns = globals()
else:
mod = import_helper(modname)
ns = mod.__dict__
try:
klass = ns[klassname]
except KeyError:
sys.stderr.write("can't find %s in %s" % (klassname,
repr(ns)))
inst = klass()
else:
raise ValueError, "expected class info: %s" % repr(klass_info)
state = u.load()
inst.__setstate__(state)
return inst
def load_state(self, state):
'''Load an image_set_list's state from the string returned from save_state'''
self.__image_sets = []
self.__image_sets_by_key = {}
# Make a safe unpickler
p = Unpickler(StringIO(state))
def find_global(module_name, class_name):
logger.debug("Pickler wants %s:%s",module_name, class_name)
if (module_name not in ("numpy", "numpy.core.multiarray")):
logger.critical(
"WARNING WARNING WARNING - your batch file has asked to load %s.%s."
" If this looks in any way suspicious please contact us at www.cellprofiler.org",
module_name, class_name)
raise ValueError("Illegal attempt to unpickle class %s.%s",
(module_name, class_name))
__import__(module_name)
mod = sys.modules[module_name]
return getattr(mod, class_name)
p.find_global = find_global
count = p.load()
all_keys = [p.load() for i in range(count)]
self.__legacy_fields = p.load()
#
# Have to do in this order in order for the image set's
# legacy_fields property to hook to the right legacy_fields
#
for i in range(count):
self.get_image_set(all_keys[i])
def state(self, oid, serial, prfactory, p=''):
p = p or self.loadSerial(oid, serial)
file = StringIO(p)
unpickler = Unpickler(file)
unpickler.persistent_load = prfactory.persistent_load
class_tuple = unpickler.load()
state = unpickler.load()
return state
def state(self, oid, serial, prfactory, p=''):
p = p or self.loadSerial(oid, serial)
file = StringIO(p)
unpickler = Unpickler(file)
unpickler.find_global = find_global
unpickler.persistent_load = prfactory.persistent_load
unpickler.load() # skip the class tuple
return unpickler.load()
def state(self, oid, serial, prfactory, p=''):
p = p or self.loadSerial(oid, serial)
file = StringIO(p)
unpickler = Unpickler(file)
unpickler.find_global = find_global
unpickler.persistent_load = prfactory.persistent_load
unpickler.load() # skip the class tuple
return unpickler.load()
def oldstate(self, object, serial):
oid=object._p_oid
p = self._storage.loadSerial(oid, serial)
file=StringIO(p)
unpickler=Unpickler(file)
unpickler.persistent_load=self._persistent_load
unpickler.load()
return unpickler.load()
def state(self, oid, serial, prfactory, p=""):
p = p or self.loadSerial(oid, serial)
p = self._crs_untransform_record_data(p)
file = StringIO(p)
unpickler = Unpickler(file)
unpickler.find_global = find_global
unpickler.persistent_load = prfactory.persistent_load
unpickler.load() # skip the class tuple
return unpickler.load()
def tryToResolveConflict(self, oid, committedSerial, oldSerial, newpickle,
committedData=''):
# class_tuple, old, committed, newstate = ('',''), 0, 0, 0
try:
prfactory = PersistentReferenceFactory()
newpickle = self._crs_untransform_record_data(newpickle)
file = StringIO(newpickle)
unpickler = Unpickler(file)
unpickler.find_global = find_global
unpickler.persistent_load = prfactory.persistent_load
meta = unpickler.load()
if isinstance(meta, tuple):
klass = meta[0]
newargs = meta[1] or ()
if isinstance(klass, tuple):
klass = find_global(*klass)
else:
klass = meta
newargs = ()
if klass in _unresolvable:
raise ConflictError
newstate = unpickler.load()
inst = klass.__new__(klass, *newargs)
try:
resolve = inst._p_resolveConflict
except AttributeError:
_unresolvable[klass] = 1
raise ConflictError
old = state(self, oid, oldSerial, prfactory)
committed = state(self, oid, committedSerial, prfactory, committedData)
resolved = resolve(old, committed, newstate)
file = StringIO()
pickler = Pickler(file,1)
pickler.inst_persistent_id = persistent_id
pickler.dump(meta)
pickler.dump(resolved)
return self._crs_transform_record_data(file.getvalue(1))
except (ConflictError, BadClassName):
pass
except:
# If anything else went wrong, catch it here and avoid passing an
# arbitrary exception back to the client. The error here will mask
# the original ConflictError. A client can recover from a
# ConflictError, but not necessarily from other errors. But log
# the error so that any problems can be fixed.
logger.error("Unexpected error", exc_info=True)
raise ConflictError(oid=oid, serials=(committedSerial, oldSerial),
data=newpickle)
def readAST(filename):
with open(filename, 'rb') as f:
pk = Unpickler(f)
opcode = pk.load()
while True:
try:
name = pk.load()
ast = pk.load()
except EOFError:
break
return opcode, name, ast
class IndexFile(object):
'''Open an index file for reading.
filename - the file containing the index.
Use the get and get_all method to return objects in the index.
'''
def __init__(self, filename):
if not os.path.exists(filename):
raise IndexFileMissingError(filename)
self.filename = filename
self.handle = open(self.filename)
self.unpickler = Unpickler(self.handle)
magic = self.handle.read(8)
expected_magic = 'pdko\x00\x00\x00\x01'
if magic != expected_magic:
message = 'Magic bytes incorrect. Is %s really a pdko file?' \
% self.filename
raise IndexFormatError, message
table_offset = read_offset(self.handle)
self.handle.seek(table_offset)
self.key_dict = self.unpickler.load()
def iter_addresses(self, key):
'''Get a list of pickle addresses for the given key.'''
try:
list_offset = self.key_dict[key]
self.handle.seek(list_offset)
address_list = self.unpickler.load()
for addresses in address_list:
yield addresses
except KeyError:
return
def get(self, key, column):
'''The columnth object for all object groups under they key.'''
for addresses in self.iter_addresses(key):
offset = addresses[column]
self.handle.seek(offset)
yield self.unpickler.load()
def get_all(self, key):
'''Get the full object group count for the key.'''
for addresses in self.iter_addresses(key):
objects = []
for offset in addresses:
self.handle.seek(offset)
objects.append(self.unpickler.load())
yield tuple(objects)
def count(self, key):
'''Get the object group count for the given key.'''
return len(list(self.iter_addresses(key)))
def readAST(filename):
with open(filename, 'rb') as f:
pk = Unpickler(f)
opcode = pk.load()
asts = {}
while True:
try:
name = pk.load()
ast = pk.load()
asts[(name, opcode)] = ast
except EOFError:
break
return asts
def readAST(filename):
with open(filename, 'rb') as f:
pk = Unpickler(f)
opcode = pk.load()
print 'opcode: %02x' % opcode
while True:
try:
name = pk.load()
ast = pk.load()
print '%s\n%s\n' % (name, str(ast))
except EOFError:
break
return opcode, ast
def read_level(self, path): f = open(path, "rb") try: check_file_magic(f, self.app_magic, "level") check_file_magic(f, self.level_file_magic, "level") p = Unpickler(f) file_version = p.load() app_version = p.load() check_file_version(file_version, app_version, self.level_min_version, self.level_file_version, self.level_version_ranges) level = self.unpickle_level(p) finally: f.close() return level
def load_game(self, path):
"""Restores a saved game from the specified path."""
f = open(path, "rb")
check_file_magic(f, self.app_magic, "saved game")
check_file_magic(f, self.save_file_magic, "saved game")
p = Unpickler(f)
file_version = p.load()
app_version = p.load()
check_file_version(file_version, app_version, self.save_min_version,
self.save_file_version, self.save_version_ranges)
data = p.load()
f.close()
self.restore_save_data(data)
self.set_save_path(path)
self.unsaved_progress = False
def cloneByPickle(obj, ignore_list=()):
"""Makes a copy of a ZODB object, loading ghosts as needed.
Ignores specified objects along the way, replacing them with None
in the copy.
"""
ignore_dict = {}
for o in ignore_list:
ignore_dict[id(o)] = o
def persistent_id(ob, ignore_dict=ignore_dict):
if ignore_dict.has_key(id(ob)):
return 'ignored'
if getattr(ob, '_p_changed', 0) is None:
ob._p_changed = 0
return None
def persistent_load(ref):
assert ref == 'ignored'
# Return a placeholder object that will be replaced by
# removeNonVersionedData().
placeholder = SimpleItem()
placeholder.id = "ignored_subobject"
return placeholder
stream = StringIO()
p = Pickler(stream, 1)
p.persistent_id = persistent_id
p.dump(obj)
stream.seek(0)
u = Unpickler(stream)
u.persistent_load = persistent_load
return u.load()
def loads(self, s):
up = Unpickler(BytesIO(s))
up.persistent_load = self._get_object
try:
return up.load()
except KeyError, e:
raise UnpicklingError, "Could not find Node class for %s" % e
def validate_result(result, filter_plugins = True, print_files = False):
'''Validate cached.filelist for the given result'''
path_to_report_dir = result.get_report_dir()
path_to_file = os.path.join(path_to_report_dir, 'cached.filelist')
print "validating %s" % path_to_file
if result.isThumbnail:
print("cannot validate: thumbnail")
return None
# for this_type in dmtypes.FILESET_TYPES:
# dmfs = result.get_filestat(this_type)
# if dmfs.action_state != 'L':
# print "cannot validate: not local"
# return None
dmfs = result.get_filestat(dmtypes.SIG)
# Get the cached filelist from cached.filelist file
try:
with open(path_to_file, 'rb') as fhandle:
pickle = Unpickler(fhandle)
cached_filelist = pickle.load()
except IOError as ioerror:
print "%s" % ioerror
return None
# Get a list of files on the filesystem currently
dirs = [dmfs.result.get_report_dir(), dmfs.result.experiment.expDir]
current_fs_filelist = get_walk_filelist(dirs)
# Ignore plugin_out directories
if filter_plugins:
current_fs_filelist = [filename for filename in current_fs_filelist if not '/plugin_out' in filename]
# Ignore the cached.filelist file
current_fs_filelist = [filename for filename in current_fs_filelist if not 'cached.filelist' in filename]
# Ignore the status.txt file
current_fs_filelist = [filename for filename in current_fs_filelist if not 'status.txt' in filename]
# Ignore the serialized_*.json file
current_fs_filelist = [filename for filename in current_fs_filelist if not 'serialized_' in filename]
# See if there are differences
#leftovers = list(set(cached_filelist) - set(current_fs_filelist))
#N.B. This difference here will tell us, "Of the files in the filesystem right now, how many are NOT in the cached.filelist file"
#Even if the cached.filelist contains more files than are currently on the filesystem.
#I am thinking this means we do not care if any action_state is not 'L'. It doesn't matter because we are looking for deficient
#cached.filelist.
leftovers = list(set(current_fs_filelist) - set(cached_filelist))
if print_files:
for i, item in enumerate(leftovers):
if not i: print "FILES MISSING FROM CACHED.FILELIST:"
print item
else:
if len(leftovers) > 0:
print "FILES MISSING FROM CACHED.FILELIST: %d" % len(leftovers)
print "- %s\n" % ("Not valid" if len(leftovers) > 0 else "Valid")
return None
def __getitem__(self, oid, tt=type(())):
obj = self._cache.get(oid, None)
if obj is not None:
return obj
__traceback_info__ = (oid)
self.before_load()
p, serial = self._storage.load(oid, self._version)
__traceback_info__ = (oid, p)
file=StringIO(p)
unpickler=Unpickler(file)
# unpickler.persistent_load=self._persistent_load
try:
classification = unpickler.load()
except:
raise ("Could not load oid %s. Pickled data in traceback info may "
"contain clues." % (oid))
osio = self._get_osio()
obj = osio.new_instance(oid, classification)
assert obj is not None
obj._p_oid=oid
obj._p_jar=self
obj._p_changed=None
self._set_serial(obj, serial)
self._cache[oid] = obj
if oid == osio.conf.oid_gen.root_oid:
self._root_=obj # keep a ref
return obj
def cloneByPickle(obj, ignore_list=()):
"""Makes a copy of a ZODB object, loading ghosts as needed.
Ignores specified objects along the way, replacing them with None
in the copy.
"""
ignore_dict = {}
for o in ignore_list:
ignore_dict[id(o)] = o
def persistent_id(ob, ignore_dict=ignore_dict):
if ignore_dict.has_key(id(ob)):
return 'ignored'
if getattr(ob, '_p_changed', 0) is None:
ob._p_changed = 0
return None
def persistent_load(ref):
assert ref == 'ignored'
# Return a placeholder object that will be replaced by
# removeNonVersionedData().
placeholder = SimpleItem()
placeholder.id = "ignored_subobject"
return placeholder
stream = StringIO()
p = Pickler(stream, 1)
p.persistent_id = persistent_id
p.dump(obj)
stream.seek(0)
u = Unpickler(stream)
u.persistent_load = persistent_load
return u.load()
def got_data(self, port_agent_packet):
"""
Called by the instrument connection when data is available.
Also add data to the chunker and when received call got_chunk
to publish results.
"""
data_length = port_agent_packet.get_data_length()
data = port_agent_packet.get_data()
timestamp = port_agent_packet.get_timestamp()
log.debug("Got Data: %s" % data)
log.debug("Add Port Agent Timestamp: %s" % timestamp)
unpickler = Unpickler(StringIO(data))
# Disable class unpickling, for security; record should be all
# built-in types. Note this only works with cPickle.
unpickler.find_global = None
# pkt is an antelope.Pkt.Packet object converted to a dict. Refer to
# the documentation for the Antelope Python bindings for compelete
# details.
pkt = unpickler.load()
for particle in self._particle_factory(pkt, timestamp):
self._publish_particle(particle)
def __getitem__(self, oid, tt=type(())):
obj = self._cache.get(oid, None)
if obj is not None:
return obj
__traceback_info__ = (oid)
self.before_load()
p, serial = self._storage.load(oid, self._version)
__traceback_info__ = (oid, p)
file = StringIO(p)
unpickler = Unpickler(file)
# unpickler.persistent_load=self._persistent_load
try:
classification = unpickler.load()
except:
raise ("Could not load oid %s. Pickled data in traceback info may "
"contain clues." % (oid))
osio = self._get_osio()
obj = osio.new_instance(oid, classification)
assert obj is not None
obj._p_oid = oid
obj._p_jar = self
obj._p_changed = None
self._set_serial(obj, serial)
self._cache[oid] = obj
if oid == osio.conf.oid_gen.root_oid:
self._root_ = obj # keep a ref
return obj
def validateSource(self):
skip_to_pos = 0
if os.path.exists(self.pickle):
upfh = open(self.pickle, "rb")
unpickler = Unpickler(upfh)
old_opt, old_pos = unpickler.load()
if self.opt == old_opt:
skip_to_pos = old_pos
for i in range(0, skip_to_pos, 1):
sys.stdout.write(".")
pos = -1
files = self.files['humans'].keys()
files.sort()
cp = ConfigParser()
cp.read(os.path.join(path("config"), "test.cnf"))
validator_path = cp.get("validation", "validator")
csl_schema_path = cp.get("validation", "schema")
cslm_schema_path = cp.get("validation", "schema-m")
for filename in files:
pos += 1
if pos < skip_to_pos: continue
p = self.files['humans'][filename]
test = CslTest(opt, p, filename, pos=pos)
test.parse()
test.validate(validator_path, csl_schema_path, cslm_schema_path)
if os.path.exists(self.pickle):
os.unlink(self.pickle)
def _cloneByPickle(self, obj):
"""Returns a deep copy of a ZODB object, loading ghosts as needed.
"""
modifier = getToolByName(self, 'portal_modifier')
callbacks = modifier.getOnCloneModifiers(obj)
if callbacks is not None:
pers_id, pers_load, inside_orefs, outside_orefs = callbacks[0:4]
else:
inside_orefs, outside_orefs = (), ()
stream = StringIO()
p = Pickler(stream, 1)
if callbacks is not None:
p.persistent_id = pers_id
cmf_uid = getattr(obj, 'cmf_uid', None)
if IUniqueIdAnnotation.providedBy(cmf_uid):
setattr(obj, 'cmf_uid', cmf_uid())
try:
p.dump(aq_base(obj))
except TypeError:
# just try again, this then seems to work
# WTF?
p.dump(aq_base(obj))
approxSize = stream.tell()
stream.seek(0)
u = Unpickler(stream)
if callbacks is not None:
u.persistent_load = pers_load
return approxSize, u.load(), inside_orefs, outside_orefs
def got_data(self, port_agent_packet):
"""
Called by the instrument connection when data is available.
Also add data to the chunker and when received call got_chunk
to publish results.
"""
data_length = port_agent_packet.get_data_length()
data = port_agent_packet.get_data()
timestamp = port_agent_packet.get_timestamp()
log.debug("Got Data: %s" % data)
log.debug("Add Port Agent Timestamp: %s" % timestamp)
unpickler = Unpickler(StringIO(data))
# Disable class unpickling, for security; record should be all
# built-in types. Note this only works with cPickle.
unpickler.find_global = None
# pkt is an antelope.Pkt.Packet object converted to a dict. Refer to
# the documentation for the Antelope Python bindings for compelete
# details.
pkt = unpickler.load()
for particle in self._particle_factory(pkt, timestamp):
self._publish_particle(particle)
def setklassstate(self, object):
try:
oid=object._p_oid
__traceback_info__=oid
p, serial = self._storage.load(oid, self._version)
file=StringIO(p)
unpickler=Unpickler(file)
unpickler.persistent_load=self._persistent_load
copy = unpickler.load()
klass, args = copy
if klass is not ExtensionKlass:
LOG('ZODB',ERROR,
"Unexpected klass when setting class state on %s"
% getattr(object,'__name__','(?)'))
return
copy=apply(klass,args)
object.__dict__.clear()
object.__dict__.update(copy.__dict__)
object._p_oid=oid
object._p_jar=self
object._p_changed=0
object._p_serial=serial
except:
LOG('ZODB',ERROR, 'setklassstate failed', error=sys.exc_info())
raise
def _unpickle(pickled):
""" Unpickles a string and catch all types of errors it can throw,
to raise only NotReadableJobError in case of error.
OpenERP stores the text fields as 'utf-8', so we specify the encoding.
`loads()` may raises many types of exceptions (AttributeError,
IndexError, TypeError, KeyError, ...). They are all catched and
raised as `NotReadableJobError`).
Pickle could be exploited by an attacker who would write a value in a job
that would run arbitrary code when unpickled. This is why we set a custom
``find_global`` method on the ``Unpickler``, only jobs and a whitelist of
classes/functions are allowed to be unpickled (plus the builtins types).
"""
def restricted_find_global(mod_name, fn_name):
__import__(mod_name)
mod = sys.modules[mod_name]
fn = getattr(mod, fn_name)
if not (fn in JOB_REGISTRY or fn in _UNPICKLE_WHITELIST):
raise UnpicklingError(
'{}.{} is not allowed in jobs'.format(mod_name, fn_name)
)
return fn
unpickler = Unpickler(StringIO(pickled))
unpickler.find_global = restricted_find_global
try:
unpickled = unpickler.load()
except (StandardError, UnpicklingError):
raise NotReadableJobError('Could not unpickle.', pickled)
return unpickled
def replay(self, name):
replay_file_path = os.path.join(PROJECTS, self.name, "replays", name)
replay = None
with open(replay_file_path, "r") as fp:
upkl = Unpickler(fp)
replay = upkl.load()
return replay
def getNewState(self, file):
# Would like to do load(file) here... but it doesn't work with universal line endings, see Python bug 1724366
from cStringIO import StringIO
unpickler = Unpickler(StringIO(file.read()))
# Magic to keep us backward compatible in the face of packages changing...
unpickler.find_global = self.findGlobal
return unpickler.load()
def unpickle(file_path=None):
"""Load pickled Python objects from a file.
Almost like ``cPickle.load(open(file_path))``, but also loads object saved
with older versions of Eelbrain, and allows using a system file dialog to
select a file.
Parameters
----------
file_path : None | str
Path to a pickled file. If None, a system file dialog will be used. If
the user cancels the file dialog, a RuntimeError is raised.
"""
if file_path is None:
filetypes = [("Pickles (*.pickled)", '*.pickled'), ("All files", '*')]
file_path = ui.ask_file("Select File to Unpickle", "Select a pickled "
"file to unpickle", filetypes)
if file_path is False:
raise RuntimeError("User canceled")
if not os.path.exists(file_path):
new_path = os.extsep.join((file_path, 'pickled'))
if os.path.exists(new_path):
file_path = new_path
with open(file_path, 'r') as fid:
unpickler = Unpickler(fid)
unpickler.find_global = map_paths
obj = unpickler.load()
return obj
def deepCopy(obj):
stream = StringIO()
p = Pickler(stream, 1)
p.dump(obj)
stream.seek(0)
u = Unpickler(stream)
return u.load()
def getNewState(cls, file):
# Would like to do load(file) here... but it doesn't work with universal line endings, see Python bug 1724366
from cStringIO import StringIO
unpickler = Unpickler(StringIO(file.read()))
# Magic to keep us backward compatible in the face of packages changing...
unpickler.find_global = cls.findGlobal
return unpickler.load()
def validateSource(self):
skip_to_pos = 0
if os.path.exists(self.pickle):
upfh = open(self.pickle, "rb")
unpickler = Unpickler(upfh)
old_opt,old_pos = unpickler.load()
if self.opt == old_opt:
skip_to_pos = old_pos
for i in range(0,skip_to_pos,1):
sys.stdout.write(".")
pos = -1
files = self.files['humans'].keys()
files.sort()
cp = ConfigParser()
cp.read(os.path.join(path("config"), "test.cnf"))
validator_path = cp.get("validation", "validator")
csl_schema_path = cp.get("validation", "schema")
cslm_schema_path = cp.get("validation", "schema-m")
for filename in files:
pos += 1
if pos < skip_to_pos: continue
p = self.files['humans'][filename]
test = CslTest(opt,p,filename,pos=pos)
test.parse()
test.validate(validator_path, csl_schema_path, cslm_schema_path)
if os.path.exists( self.pickle ):
os.unlink(self.pickle)
def unpickle(file_path=None):
"""Load pickled Python objects from a file.
Almost like ``cPickle.load(open(file_path))``, but also loads object saved
with older versions of Eelbrain, and allows using a system file dialog to
select a file.
Parameters
----------
file_path : None | str
Path to a pickled file. If None (default), a system file dialog will be
shown. If the user cancels the file dialog, a RuntimeError is raised.
"""
if file_path is None:
filetypes = [("Pickles (*.pickled)", '*.pickled'), ("All files", '*')]
file_path = ui.ask_file("Select File to Unpickle", "Select a pickled "
"file to unpickle", filetypes)
if file_path is False:
raise RuntimeError("User canceled")
else:
print repr(file_path)
else:
file_path = os.path.expanduser(file_path)
if not os.path.exists(file_path):
new_path = os.extsep.join((file_path, 'pickled'))
if os.path.exists(new_path):
file_path = new_path
with open(file_path, 'r') as fid:
unpickler = Unpickler(fid)
unpickler.find_global = map_paths
obj = unpickler.load()
return obj
def loads(self, s):
up = Unpickler(BytesIO(s))
up.persistent_load = self._get_object
try:
return up.load()
except KeyError, e:
raise UnpicklingError("Could not find Node class for %s" % e)
def deserialize(self, message, task_id=None):
"""Deserialize an object
:param message: A serialized object (string).
:param deferred: When true load deferreds. When false
raise an error if the message contains deferreds.
"""
fail = []
if task_id is None:
def persistent_load(task_id):
raise UnpicklingError('message contained references to '
'external objects: %s' % task_id)
else:
args = self._queue.get_arguments(task_id)
args = {k: loads(v) for k, v in args.items()}
def persistent_load(arg_id):
value = args[arg_id]
if isinstance(value, TaskFailure):
fail.append(value)
return value
data = StringIO(message)
pickle = Unpickler(data)
pickle.persistent_load = persistent_load
obj = pickle.load()
if fail and not obj.on_error_pass:
# TODO detect errors earlier, fail earlier, cancel enqueued tasks
self.set_result(obj, fail[0])
obj = None
return obj
def deserialize(self, message, task_id=None):
"""Deserialize an object
:param message: A serialized object (string).
:param deferred: When true load deferreds. When false
raise an error if the message contains deferreds.
"""
fail = []
if task_id is None:
def persistent_load(task_id):
raise UnpicklingError('message contained references to '
'external objects: %s' % task_id)
else:
args = self._queue.get_arguments(task_id)
args = {k: loads(v) for k, v in args.items()}
def persistent_load(arg_id):
value = args[arg_id]
if isinstance(value, TaskFailure):
fail.append(value)
return value
data = StringIO(message)
pickle = Unpickler(data)
pickle.persistent_load = persistent_load
obj = pickle.load()
if fail and not obj.on_error_pass:
# TODO detect errors earlier, fail earlier, cancel enqueued tasks
self.set_result(obj, fail[0])
obj = None
return obj
def pickle_load(file_name):
f = open(file_name, "rb")
obj = None
if f != None:
u = Unpickler(f)
obj = u.load()
f.close()
return obj
def load(self, model_path):
"""
Load the pickled classifier model from disk
:param model_path: path to the model
:type model_path: str
"""
try:
with open(model_path) as f:
pickle = Unpickler(f)
self.classifiers = pickle.load()
with open(model_path.replace('.m', '.vec')) as f:
pickle = Unpickler(f)
self.vectorizer = pickle.load()
except IOError:
self.logger.info('Could not load model: {}'.format(model_path))
def deepcopy(obj):
"""Makes a deep copy of the object using the pickle mechanism.
"""
stream = StringIO()
p = Pickler(stream, 1)
p.dump(aq_base(obj))
stream.seek(0)
u = Unpickler(stream)
return u.load()
def server_decode(msg):
"""Decodes msg and returns its parts"""
unpickler = Unpickler(StringIO(msg))
unpickler.find_global = server_find_global
try:
return unpickler.load() # msgid, flags, name, args
except:
log("can't decode message: %s" % short_repr(msg), level=logging.ERROR)
raise
def get_action_param_var(pfilename):
'''
Argument is name of file to unpickle. Return value is dictionary value.
'''
from cPickle import Unpickler
with open(pfilename,'rb') as fileh:
pickle = Unpickler(fileh)
list_of_dict_files = pickle.load()
return list_of_dict_files
'''
def get_action_param_file(pfilename):
'''
Argument is name of file to unpickle. Return value is dictionary value.
'''
from cPickle import Unpickler
fileh = open(pfilename, 'rb')
pickle = Unpickler(fileh)
list_of_dict_files = pickle.load()
fileh.close()
return list_of_dict_files