def write(self, io_file, value):
if self._nullable:
if value is None:
BooleanWrapper().write(io_file, False)
return
else:
BooleanWrapper().write(io_file, True)
if self._mode == "utf-8":
ba = value.encode('utf-8')
elif self._mode == "utf-16":
ba = value.encode('utf-16-be')
elif self._mode == "binary":
if isinstance(value, BytesIO):
ba = value.getvalue()
else:
if six.PY2:
ba = bytes(value)
elif six.PY3:
ba = bytes(value, "utf-8")
else:
raise TypeError("Internal mode {} not recognized".format(
self._mode))
IntegerWrapper(32).write(io_file, len(ba))
io_file.write(ba)
def write(self, io_file, value):
if self._nullable:
if value is None:
BooleanWrapper().write(io_file, False)
return
else:
BooleanWrapper().write(io_file, True)
io_file.write(value.get_bytes())
def serialize_reference_counting(self, dc_obj, io_file):
""" TODO: IMPORTANT: this should be removed in new serialization by using paddings to directly access reference counters inside
metadata. """
"""
@postcondition: Serialize reference counting (garbage collector information)
@param dc_obj: dc object with ref counting
@param io_file: Buffer in which to serialize
@param reference_counting: Reference counting to serialize
"""
self.external_references = 0
if dc_obj.get_alias() is not None and dc_obj.get_alias() != "":
logger.trace("Found alias reference")
self.external_references = self.external_references + 1
cur_dataclay_id = getRuntime().get_dataclay_id()
if dc_obj.get_replica_locations() is not None and len(
dc_obj.get_replica_locations()) != 0:
for replica_loc in dc_obj.get_replica_locations():
replica_dataclay_id = getRuntime(
).get_execution_environment_info(
replica_loc).dataclay_instance_id
if replica_dataclay_id != cur_dataclay_id:
logger.trace("Found federation reference")
self.external_references = self.external_references + 1
break
logger.trace(
f"Serializing reference counting external references = {self.external_references}"
)
IntegerWrapper().write(io_file, self.external_references)
IntegerWrapper().write(io_file, len(self.reference_counting))
for location, ref_counting_in_loc in self.reference_counting.items():
if location is None:
BooleanWrapper().write(io_file, True)
else:
BooleanWrapper().write(io_file, False)
StringWrapper().write(io_file, str(location))
IntegerWrapper().write(io_file, len(ref_counting_in_loc))
for oid, counter in ref_counting_in_loc.items():
StringWrapper().write(io_file, str(oid))
IntegerWrapper().write(io_file, counter)
def serialize_reference_counting(self, referrer_oid, io_file):
""" TODO: IMPORTANT: this should be removed in new serialization by using paddings to directly access reference counters inside
metadata. """
"""
@postcondition: Serialize reference counting (garbage collector information)
@param referrer_oid: ID of referrer object
@param io_file: Buffer in which to serialize
@param reference_counting: Reference counting to serialize
"""
IntegerWrapper().write(io_file, len(self.reference_counting))
for location, ref_counting_in_loc in self.reference_counting.items():
if location is None:
BooleanWrapper().write(io_file, True)
else:
BooleanWrapper().write(io_file, False)
StringWrapper().write(io_file, str(location))
IntegerWrapper().write(io_file, len(ref_counting_in_loc))
for oid, counter in ref_counting_in_loc.items():
StringWrapper().write(io_file, str(oid))
IntegerWrapper().write(io_file, counter)
def read(self, io_file):
if self._nullable:
is_not_null = BooleanWrapper().read(io_file)
if not is_not_null:
return None
size = IntegerWrapper(32).read(io_file)
ba = io_file.read(size)
if self._mode == "utf-8":
return ba.decode('utf-8')
elif self._mode == "utf-16":
return ba.decode('utf-16-be')
elif self._mode == "binary":
return ba
else:
raise TypeError("Internal mode {} not recognized".format(
self._mode))
def read(self, io_file):
from dataclay.util.management.classmgr.Utils import serialization_types
try:
return serialization_types[self._signature].read(io_file)
except KeyError:
pass
# numpy have their own special ultra-fast serialization
if self._signature.startswith(self.NUMPY_SIGNATURE):
import numpy as np
# Ignoring field size, as numpy is selfcontained in that matter
_ = IntegerWrapper(32).read(io_file)
return np.load(io_file, allow_pickle=False)
# anything is also a special case, also all its alias
if self._signature == self.ANYTHING_SIGNATURE or \
self._signature == self.STORAGEOBJECT_SIGNATURE:
field_size = IntegerWrapper(32).read(io_file)
logger.debug("Deserializing DataClayObject from pickle")
return pickle.loads(io_file.read(field_size))
# Everything shoulda be a python type...
if not self._signature.startswith(self.PYTHON_PREFIX):
# ... except the fallbacks (mostly for subtypes like lists of persistent objects)
# TODO: Check pickle fallback or ignore it completely
field_size = IntegerWrapper(32).read(io_file)
return pickle.loads(io_file.read(field_size))
subtype = self._signature[len(self.PYTHON_PREFIX):]
sequence_match = self.SEQUENCE_REGEX.match(subtype)
mapping_match = self.MAPPING_REGEX.match(subtype)
if sequence_match:
gd = sequence_match.groupdict()
logger.debug("Deserializing a Python Sequence with the following match: %s", gd)
if gd["subtype"]:
instances_type = PyTypeWildcardWrapper(gd["subtype"], pickle_fallback=True)
else: # list without subtypes information
instances_type = PyTypeWildcardWrapper(self.ANYTHING_SIGNATURE)
ret = list()
size = IntegerWrapper(32).read(io_file)
logger.debug("### READ SIZE OF SEQUENCE MATCH: %i", size)
for i in range(size):
if BooleanWrapper().read(io_file):
ret.append(instances_type.read(io_file))
else:
ret.append(None)
if gd["base_type"] == "tuple":
logger.debug("Returning deserialized Python tuple")
return tuple(ret)
else:
logger.debug("Returning deserialized Python list")
return ret
elif mapping_match:
gd = mapping_match.groupdict()
logger.debug("Deserializing a Python mapping with the following match: %s", gd)
if gd["keytype"] and gd["valuetype"]:
key_type = PyTypeWildcardWrapper(gd["keytype"], pickle_fallback=True)
value_type = PyTypeWildcardWrapper(gd["valuetype"], pickle_fallback=True)
else:
# dict without subtypes information
key_type = PyTypeWildcardWrapper(self.ANYTHING_SIGNATURE)
value_type = PyTypeWildcardWrapper(self.ANYTHING_SIGNATURE)
ret = dict()
size = IntegerWrapper(32).read(io_file)
for i in range(size):
if BooleanWrapper().read(io_file):
key = key_type.read(io_file)
else:
key = None
if BooleanWrapper().read(io_file):
ret[key] = value_type.read(io_file)
else:
ret[key] = None
logger.debug("Returning deserialized Python map")
return ret
elif subtype == self.STR_SIGNATURE:
if six.PY2:
return StringWrapper('binary').read(io_file)
elif six.PY3:
return StringWrapper('utf-8').read(io_file)
elif subtype == self.UNICODE_SIGNATURE:
return StringWrapper('utf-16').read(io_file)
else:
raise NotImplementedError("Python types supported at the moment: "
"list and mappings (but not `%s`), sorry" % subtype)
def write(self, io_file, value):
value = safe_wait_if_compss_future(value)
from dataclay.util.management.classmgr.Utils import serialization_types
try:
serialization_types[self._signature].write(io_file, value)
return
except KeyError:
pass
# numpy have their own special ultra-fast serialization
if self._signature.startswith(self.NUMPY_SIGNATURE):
import numpy as np
with size_tracking(io_file):
np.save(io_file, value)
return
# anything is also a special case, also all its alias
if self._signature == self.ANYTHING_SIGNATURE or \
self._signature == self.STORAGEOBJECT_SIGNATURE:
s = pickle.dumps(value, protocol=-1)
IntegerWrapper(32).write(io_file, len(s))
io_file.write(s)
return
# Everything shoulda be a python type...
if not self._signature.startswith(self.PYTHON_PREFIX):
# ... except the fallbacks (mostly for subtypes like lists of persistent objects)
# TODO: Check pickle fallback or ignore it completely
s = pickle.dumps(value, protocol=-1)
IntegerWrapper(32).write(io_file, len(s))
io_file.write(s)
return
# Now everything must be a python type
assert self._signature.startswith(self.PYTHON_PREFIX), \
"Signature for Python types is expected to start with " \
"'python'. Found signature: %s" % self._signature
subtype = self._signature[len(self.PYTHON_PREFIX):]
sequence_match = self.SEQUENCE_REGEX.match(subtype)
mapping_match = self.MAPPING_REGEX.match(subtype)
if sequence_match:
gd = sequence_match.groupdict()
logger.debug("Serializing a Python Sequence with the following match: %s", gd)
if gd["subtype"]:
instances_type = PyTypeWildcardWrapper(gd["subtype"], pickle_fallback=True)
else: # list without subtypes information
instances_type = PyTypeWildcardWrapper(self.ANYTHING_SIGNATURE)
IntegerWrapper(32).write(io_file, len(value))
for elem in value:
if elem is None:
BooleanWrapper().write(io_file, False)
else:
BooleanWrapper().write(io_file, True)
instances_type.write(io_file, elem)
elif mapping_match:
gd = mapping_match.groupdict()
logger.debug("Serializing a Python Mapping with the following match: %s", gd)
if gd["keytype"] and gd["valuetype"]:
key_type = PyTypeWildcardWrapper(gd["keytype"], pickle_fallback=True)
value_type = PyTypeWildcardWrapper(gd["valuetype"], pickle_fallback=True)
else: # dict without subtypes information
key_type = PyTypeWildcardWrapper(self.ANYTHING_SIGNATURE)
value_type = PyTypeWildcardWrapper(self.ANYTHING_SIGNATURE)
IntegerWrapper(32).write(io_file, len(value))
for k, v in value.items():
if k is None:
BooleanWrapper().write(io_file, False)
else:
BooleanWrapper().write(io_file, True)
key_type.write(io_file, k)
if v is None:
BooleanWrapper().write(io_file, False)
else:
# ToDo remove this when COMPSs behaves correctly with compss_wait_on(dict_instance)
v = safe_wait_if_compss_future(v)
BooleanWrapper().write(io_file, True)
value_type.write(io_file, v)
elif subtype == self.STR_SIGNATURE:
if six.PY2:
StringWrapper('utf-8').write(io_file, value)
elif six.PY3:
StringWrapper('binary').write(io_file, value)
elif subtype == self.UNICODE_SIGNATURE:
StringWrapper('utf-16').write(io_file, value)
else:
raise NotImplementedError("Python types supported at the moment: "
"list and mappings (but not `%s`), sorry" % subtype)
def deserialize(self, io_file, iface_bitmaps, metadata,
cur_deserialized_python_objs):
"""Reciprocal to serialize."""
logger.verbose("Deserializing object %s", str(self.get_object_id()))
# Put slow debugging info inside here:
#
# NOTE: new implementation of ExecutionGateway assert is not needed and wrong
# if logger.isEnabledFor(DEBUG):
# klass = self.__class__
# logger.debug("Deserializing instance %r from class %s",
# self, klass.__name__)
# logger.debug("The previous class is from module %s, in file %s",
# klass.__module__, inspect.getfile(klass))
# logger.debug("The class extradata is:\n%s", klass._dclay_class_extradata)
# assert klass._dclay_class_extradata == self._dclay_class_extradata
#
# LOADED FLAG = TRUE only once deserialization is finished to avoid concurrent problems!
# # This may be due to race conditions. It may need to do some extra locking
# if self.__dclay_instance_extradata.loaded_flag:
# logger.debug("Loaded Flag is True")
# else:
# self.__dclay_instance_extradata.loaded_flag = True
""" reference counting """
""" discard padding """
IntegerWrapper().read(io_file)
""" deserialize master_location """
des_master_loc_str = StringWrapper().read(io_file)
if des_master_loc_str == "x":
self.__dclay_instance_extradata.master_location = None
else:
self.__dclay_instance_extradata.master_location = UUID(
des_master_loc_str)
if hasattr(self, "__setstate__"):
# The object has a user-defined deserialization method.
# Use pickle, and use that method instead
if six.PY2:
import cPickle as pickle
elif six.PY3:
import _pickle as pickle
state = pickle.loads(StringWrapper(mode="binary").read(io_file))
self.__setstate__(state)
else:
# Regular dataClay provided deserialization
# Start by getting the properties
properties = sorted(self.get_class_extradata().properties.values(),
key=attrgetter('position'))
logger.trace("Tell io_file before loop: %s", io_file.tell())
logger.verbose("Deserializing list of properties: %s", properties)
for p in properties:
logger.trace("Tell io_file in loop: %s", io_file.tell())
not_null = BooleanWrapper().read(io_file)
value = None
if not_null:
logger.debug("Not null property %s", p.name)
if isinstance(p.type, UserType):
try:
logger.debug("Property %s is an association",
p.name)
value = DeserializationLibUtilsSingleton.deserialize_association(
io_file, iface_bitmaps, metadata,
cur_deserialized_python_objs, getRuntime())
except KeyError as e:
logger.error('Failed to deserialize association',
exc_info=True)
else:
try:
upck = Unpickler(io_file)
upck.persistent_load = PersistentLoadPicklerHelper(
metadata, cur_deserialized_python_objs,
getRuntime())
value = upck.load()
except:
traceback.print_exc()
logger.debug("Setting value %s for property %s", value, p.name)
object.__setattr__(self,
"%s%s" % (DCLAY_PROPERTY_PREFIX, p.name),
value)
""" reference counting bytes here """
""" TODO: discard bytes? """
def serialize(self, io_file, ignore_user_types, iface_bitmaps,
cur_serialized_objs, pending_objs, reference_counting):
# Reference counting information
# First integer represent the position in the buffer in which
# reference counting starts. This is done to avoid "holding"
# unnecessary information during a store or update in disk.
# in new serialization, this will be done through padding
# TODO: use padding instead once new serialization is implemented
IntegerWrapper().write(io_file, 0)
cur_master_loc = self.get_master_location()
if cur_master_loc is not None:
StringWrapper().write(io_file, str(cur_master_loc))
else:
StringWrapper().write(io_file, str("x"))
if hasattr(self, "__getstate__"):
# The object has a user-defined serialization method.
# Use that
dco_extradata = self.__dclay_instance_extradata
last_loaded_flag = dco_extradata.loaded_flag
last_persistent_flag = dco_extradata.persistent_flag
dco_extradata.loaded_flag = True
dco_extradata.persistent_flag = False
# Use pickle to the result of the serialization
if six.PY2:
import cPickle as pickle
elif six.PY3:
import _pickle as pickle
state = pickle.dumps(self.__getstate__(), protocol=-1)
# Leave the previous value, probably False & True`
dco_extradata.loaded_flag = last_loaded_flag
dco_extradata.persistent_flag = last_persistent_flag
StringWrapper(mode="binary").write(io_file, state)
else:
# Regular dataClay provided serialization
# Get the list of properties, making sure it is sorted
properties = sorted(self.get_class_extradata().properties.values(),
key=attrgetter('position'))
logger.verbose("Serializing list of properties: %s", properties)
for p in properties:
try:
value = object.__getattribute__(
self, "%s%s" % (DCLAY_PROPERTY_PREFIX, p.name))
except AttributeError:
value = None
logger.verbose("Serializing property %s with value %s ",
p.name, value)
if value is None:
BooleanWrapper().write(io_file, False)
else:
if isinstance(p.type, UserType):
if not ignore_user_types:
BooleanWrapper().write(io_file, True)
SerializationLibUtilsSingleton.serialize_association(
io_file, value, cur_serialized_objs,
pending_objs, reference_counting)
else:
BooleanWrapper().write(io_file, False)
else:
BooleanWrapper().write(io_file, True)
pck = Pickler(io_file, protocol=-1)
pck.persistent_id = PersistentIdPicklerHelper(
cur_serialized_objs, pending_objs,
reference_counting)
pck.dump(value)
# Reference counting
# TODO: this should be removed in new serialization
# TODO: (by using paddings to directly access reference counters inside metadata)
cur_stream_pos = io_file.tell()
io_file.seek(0)
IntegerWrapper().write(io_file, cur_stream_pos)
io_file.seek(cur_stream_pos)
reference_counting.serialize_reference_counting(
self.get_object_id(), io_file)
{% endif %}{% else %}
{% endfor %}):
raise NotImplementedError("Language Error: Method {{ func_name }} is not available for Python")
""")
# Note that the class_id of language types are null since "dataClay 2"
mapping_table = [
(("int", int, IntegerWrapper(64)), Type(
signature='J',
includes=[],
)),
(("float", float, FloatWrapper(64)), Type(
signature='D',
includes=[],
)),
(("bool", bool, BooleanWrapper()), Type(
signature='Z',
includes=[],
)),
(("None", None, NullWrapper()), Type(
signature='V',
includes=[],
)),
]
# Statically build the dictionaries for fast and easy lookup
docstring_types = dict(
starmap(lambda what, type_c: (what[0], type_c), mapping_table))
instance_types = dict(
starmap(lambda what, type_c: (what[1], type_c), mapping_table))
def read(self, io_file):
if self._nullable:
present = BooleanWrapper().read(io_file)
if not present:
return None
return uuid.UUID(bytes=str(io_file.read(16)))
