def serialize(self,
encoding: str,
*,
include: Optional[Set[str]] = None,
exclude: Optional[Set[str]] = None,
skip_defaults: bool = False) -> Union[bytes, str]:
"""Generates a serialized representation of the model
Parameters
----------
encoding : str
The serialization type, available types are: {'json', 'json-ext', 'msgpack-ext'}
include : Optional[Set[str]], optional
Fields to be included in the serialization.
exclude : Optional[Set[str]], optional
Fields to be excluded in the serialization.
skip_defaults : bool, optional
If True, skips fields that have default values provided.
Returns
-------
Union[bytes, str]
The serialized model.
"""
data = self.dict(include=include,
exclude=exclude,
skip_defaults=skip_defaults)
return serialize(data, encoding=encoding)
def dict(self,
*,
ser_kwargs: Dict[str, Any] = {},
**kwargs: Dict[str, Any]) -> Dict[str, Any]:
"""Returns object fields as a dictionary.
Parameters
----------
ser_kwargs: Optional[Dict[str, Any]]
Additional keyword arguments to pass to serialize.
**kwargs: Optional[Dict[str, Any]]
Additional keyword arguments, allow which fields to include, exclude, etc.
Returns
-------
Dict[str, Any]
Fields as a dictionary.
"""
encoding = kwargs.pop("encoding", None)
kwargs["exclude"] = (
kwargs.get("exclude", None) or
set()) | self.__config__.serialize_default_excludes # type: ignore
kwargs.setdefault(
"exclude_unset",
self.__config__.serialize_skip_defaults) # type: ignore
if self.__config__.force_skip_defaults: # type: ignore
kwargs["exclude_unset"] = True
data = super().dict(**kwargs)
if encoding is None:
return data
elif encoding == "json":
return json.loads(serialize(data, encoding=encoding, **ser_kwargs))
elif encoding == "yaml":
yaml = yaml_import(raise_error=True)
return yaml.safe_load(
serialize(data, encoding=encoding, **ser_kwargs))
else:
raise KeyError(
f"Unknown encoding type '{encoding}', valid encoding types: 'json', 'yaml'."
)
def serialize(
self,
encoding: str,
*,
include: Optional[Set[str]] = None,
exclude: Optional[Set[str]] = None,
exclude_unset: Optional[bool] = None,
exclude_defaults: Optional[bool] = None,
exclude_none: Optional[bool] = None,
**kwargs: Optional[Dict[str, Any]],
) -> Union[bytes, str]:
"""Generates a serialized representation of the model
Parameters
----------
encoding : str
The serialization type, available types are: {'json', 'json-ext', 'msgpack-ext'}
include : Optional[Set[str]], optional
Fields to be included in the serialization.
exclude : Optional[Set[str]], optional
Fields to be excluded in the serialization.
exclude_unset : Optional[bool], optional
If True, skips fields that have default values provided.
exclude_defaults: Optional[bool], optional
If True, skips fields that have set or defaulted values equal to the default.
exclude_none: Optional[bool], optional
If True, skips fields that have value ``None``.
**kwargs: Optional[Dict[str, Any]]
Additional keyword arguments to pass to serialize.
Returns
-------
Union[bytes, str]
The serialized model.
"""
fdargs = {}
if include:
fdargs["include"] = include
if exclude:
fdargs["exclude"] = exclude
if exclude_unset:
fdargs["exclude_unset"] = exclude_unset
if exclude_defaults:
fdargs["exclude_defaults"] = exclude_defaults
if exclude_none:
fdargs["exclude_none"] = exclude_none
data = self.dict(**fdargs)
return serialize(data, encoding=encoding, **kwargs)
def dict(self, **kwargs) -> Dict[str, Any]:
encoding = kwargs.pop("encoding", None)
kwargs["exclude"] = (
kwargs.get("exclude", None) or set()
) | self.__config__.serialize_default_excludes # type: ignore
kwargs.setdefault("exclude_unset", self.__config__.serialize_skip_defaults) # type: ignore
if self.__config__.force_skip_defaults: # type: ignore
kwargs["exclude_unset"] = True
data = super().dict(**kwargs)
if encoding is None:
return data
elif encoding == "json":
return json.loads(serialize(data, encoding="json"))
else:
raise KeyError(f"Unknown encoding type '{encoding}', valid encoding types: 'json'.")
def serialize(
self,
encoding: str,
*,
include: Optional[Set[str]] = None,
exclude: Optional[Set[str]] = None,
exclude_unset: Optional[bool] = None,
) -> Union[bytes, str]:
"""Generates a serialized representation of the model
Parameters
----------
encoding : str
The serialization type, available types are: {'json', 'json-ext', 'msgpack-ext'}
include : Optional[Set[str]], optional
Fields to be included in the serialization.
exclude : Optional[Set[str]], optional
Fields to be excluded in the serialization.
exclude_unset : Optional[bool], optional
If True, skips fields that have default values provided.
Returns
-------
Union[bytes, str]
The serialized model.
"""
kwargs = {}
if include:
kwargs["include"] = include
if exclude:
kwargs["exclude"] = exclude
if exclude_unset:
kwargs["exclude_unset"] = exclude_unset
data = self.dict(**kwargs)
return serialize(data, encoding=encoding)
def write(self, data):
if not isinstance(data, (str, bytes)):
data = serialize(data, self.encoding)
return super().write(data)
for driver in drivers:
folder_name = os.path.join(
temporary_directory,
f"{model['method'].lower()}_{molecule_name}_{driver}")
os.makedirs(folder_name, exist_ok=True)
input_model = {
"molecule": qcng.get_molecule(molecule_name),
"keywords": keywords,
"model": model,
"driver": driver,
}
input_model = qcel.models.ResultInput(**input_model)
with open(os.path.join(folder_name, "input.json"), "w") as handle:
handle.write(serialize(input_model, 'json'))
# Save generated infiles
prog = qcng.get_program(program)
inputs = prog.build_input(input_model, config)
with open(os.path.join(folder_name, "infiles.msgpack"), "wb") as handle:
handle.write(serialize(inputs["infiles"], 'msgpack-ext'))
# Save outfiles
ret = prog.execute(inputs)
with open(os.path.join(folder_name, "outfiles.msgpack"), "wb") as handle:
handle.write(serialize(ret[1]["outfiles"], 'msgpack-ext'))
# Save result
result = prog.parse_output(ret[1]["outfiles"], input_model)
with open(os.path.join(folder_name, "output.json"), "w") as handle:
