# coding: utf-8
"""
JSON serialization and deserialization utilities.
"""
import os
import json
import datetime
from hashlib import sha1
from collections import OrderedDict, defaultdict
from enum import Enum
from importlib import import_module
from inspect import getfullargspec
try:
import numpy as np
except ImportError:
np = None # type: ignore
try:
import bson
except ImportError:
bson = None
try:
import ruamel.yaml as yaml
except ImportError:
try:
import yaml # type: ignore
except ImportError:
yaml = None # type: ignore
__version__ = "3.0.0"
def _load_redirect(redirect_file):
try:
with open(redirect_file, "rt") as f:
d = yaml.safe_load(f)
except IOError:
# If we can't find the file
# Just use an empty redirect dict
return {}
# Convert the full paths to module/class
redirect_dict = defaultdict(dict)
for old_path, new_path in d.items():
old_class = old_path.split(".")[-1]
old_module = ".".join(old_path.split(".")[:-1])
new_class = new_path.split(".")[-1]
new_module = ".".join(new_path.split(".")[:-1])
redirect_dict[old_module][old_class] = {
"@module": new_module,
"@class": new_class,
}
return dict(redirect_dict)
[docs]class MSONable:
"""
This is a mix-in base class specifying an API for msonable objects. MSON
is Monty JSON. Essentially, MSONable objects must implement an as_dict
method, which must return a json serializable dict and must also support
no arguments (though optional arguments to finetune the output is ok),
and a from_dict class method that regenerates the object from the dict
generated by the as_dict method. The as_dict method should contain the
"@module" and "@class" keys which will allow the MontyEncoder to
dynamically deserialize the class. E.g.::
d["@module"] = self.__class__.__module__
d["@class"] = self.__class__.__name__
A default implementation is provided in MSONable, which automatically
determines if the class already contains self.argname or self._argname
attributes for every arg. If so, these will be used for serialization in
the dict format. Similarly, the default from_dict will deserialization
classes of such form. An example is given below::
class MSONClass(MSONable):
def __init__(self, a, b, c, d=1, **kwargs):
self.a = a
self.b = b
self._c = c
self._d = d
self.kwargs = kwargs
For such classes, you merely need to inherit from MSONable and you do not
need to implement your own as_dict or from_dict protocol.
New to Monty V2.0.6....
Classes can be redirected to moved implementations by putting in the old
fully qualified path and new fully qualified path into .monty.yaml in the
home folder
Example:
old_module.old_class: new_module.new_class
"""
REDIRECT = _load_redirect(
os.path.join(os.path.expanduser("~"), ".monty.yaml"))
[docs] def as_dict(self) -> dict:
"""
A JSON serializable dict representation of an object.
"""
d = {
"@module": self.__class__.__module__,
"@class": self.__class__.__name__
}
try:
parent_module = self.__class__.__module__.split('.')[0]
module_version = import_module(parent_module).__version__ # type: ignore
d["@version"] = u"{}".format(module_version)
except (AttributeError, ImportError):
d["@version"] = None # type: ignore
spec = getfullargspec(self.__class__.__init__)
args = spec.args
def recursive_as_dict(obj):
if isinstance(obj, (list, tuple)):
return [recursive_as_dict(it) for it in obj]
if isinstance(obj, dict):
return {kk: recursive_as_dict(vv) for kk, vv in obj.items()}
if hasattr(obj, "as_dict"):
return obj.as_dict()
return obj
for c in args:
if c != "self":
try:
a = self.__getattribute__(c)
except AttributeError:
try:
a = self.__getattribute__("_" + c)
except AttributeError:
raise NotImplementedError(
"Unable to automatically determine as_dict "
"format from class. MSONAble requires all "
"args to be present as either self.argname or "
"self._argname, and kwargs to be present under"
"a self.kwargs variable to automatically "
"determine the dict format. Alternatively, "
"you can implement both as_dict and from_dict.")
d[c] = recursive_as_dict(a)
if hasattr(self, "kwargs"):
# type: ignore
d.update(**getattr(self, "kwargs")) # pylint: disable=E1101
if spec.varargs is not None and getattr(self, spec.varargs, None) is not None:
d.update({spec.varargs: getattr(self, spec.varargs)})
if hasattr(self, "_kwargs"):
d.update(**getattr(self, "_kwargs")) # pylint: disable=E1101
if isinstance(self, Enum):
d.update({"value": self.value}) # pylint: disable=E1101
return d
[docs] @classmethod
def from_dict(cls, d):
"""
:param d: Dict representation.
:return: MSONable class.
"""
decoded = {
k: MontyDecoder().process_decoded(v)
for k, v in d.items() if not k.startswith("@")
}
return cls(**decoded)
[docs] def to_json(self) -> str:
"""
Returns a json string representation of the MSONable object.
"""
return json.dumps(self, cls=MontyEncoder)
[docs] def unsafe_hash(self):
"""
Returns an hash of the current object. This uses a generic but low
performance method of converting the object to a dictionary, flattening
any nested keys, and then performing a hash on the resulting object
"""
def flatten(obj, seperator="."):
# Flattens a dictionary
flat_dict = {}
for key, value in obj.items():
if isinstance(value, dict):
flat_dict.update({
seperator.join([key, _key]): _value
for _key, _value in flatten(value).items()
})
elif isinstance(value, list):
list_dict = {
"{}{}{}".format(key, seperator, num): item
for num, item in enumerate(value)
}
flat_dict.update(flatten(list_dict))
else:
flat_dict[key] = value
return flat_dict
ordered_keys = sorted(flatten(jsanitize(self.as_dict())).items(),
key=lambda x: x[0])
ordered_keys = [item for item in ordered_keys if "@" not in item[0]]
return sha1(json.dumps(OrderedDict(ordered_keys)).encode("utf-8"))
[docs]class MontyEncoder(json.JSONEncoder):
"""
A Json Encoder which supports the MSONable API, plus adds support for
numpy arrays, datetime objects, bson ObjectIds (requires bson).
Usage::
# Add it as a *cls* keyword when using json.dump
json.dumps(object, cls=MontyEncoder)
"""
[docs] def default(self, o) -> dict: # pylint: disable=E0202
"""
Overriding default method for JSON encoding. This method does two
things: (a) If an object has a to_dict property, return the to_dict
output. (b) If the @module and @class keys are not in the to_dict,
add them to the output automatically. If the object has no to_dict
property, the default Python json encoder default method is called.
Args:
o: Python object.
Return:
Python dict representation.
"""
if isinstance(o, datetime.datetime):
return {
"@module": "datetime",
"@class": "datetime",
"string": o.__str__()
}
if np is not None:
if isinstance(o, np.ndarray):
if str(o.dtype).startswith('complex'):
return {
"@module": "numpy",
"@class": "array",
"dtype": o.dtype.__str__(),
"data": [o.real.tolist(),
o.imag.tolist()]
}
return {
"@module": "numpy",
"@class": "array",
"dtype": o.dtype.__str__(),
"data": o.tolist()
}
if isinstance(o, np.generic):
return o.item()
if bson is not None:
if isinstance(o, bson.objectid.ObjectId):
return {
"@module": "bson.objectid",
"@class": "ObjectId",
"oid": str(o)
}
try:
d = o.as_dict()
if "@module" not in d:
d["@module"] = u"{}".format(o.__class__.__module__)
if "@class" not in d:
d["@class"] = u"{}".format(o.__class__.__name__)
if "@version" not in d:
try:
parent_module = o.__class__.__module__.split('.')[0]
module_version = import_module(parent_module).__version__ # type: ignore
d["@version"] = u"{}".format(module_version)
except (AttributeError, ImportError):
d["@version"] = None
return d
except AttributeError:
return json.JSONEncoder.default(self, o)
[docs]class MontyDecoder(json.JSONDecoder):
"""
A Json Decoder which supports the MSONable API. By default, the
decoder attempts to find a module and name associated with a dict. If
found, the decoder will generate a Pymatgen as a priority. If that fails,
the original decoded dictionary from the string is returned. Note that
nested lists and dicts containing pymatgen object will be decoded correctly
as well.
Usage:
# Add it as a *cls* keyword when using json.load
json.loads(json_string, cls=MontyDecoder)
"""
[docs] def process_decoded(self, d):
"""
Recursive method to support decoding dicts and lists containing
pymatgen objects.
"""
if isinstance(d, dict):
if "@module" in d and "@class" in d:
modname = d["@module"]
classname = d["@class"]
if classname in MSONable.REDIRECT.get(modname, {}):
modname = MSONable.REDIRECT[modname][classname]["@module"]
classname = MSONable.REDIRECT[modname][classname]["@class"]
else:
modname = None
classname = None
if modname and modname not in ["bson.objectid", "numpy"]:
if modname == "datetime" and classname == "datetime":
try:
dt = datetime.datetime.strptime(
d["string"], "%Y-%m-%d %H:%M:%S.%f")
except ValueError:
dt = datetime.datetime.strptime(
d["string"], "%Y-%m-%d %H:%M:%S")
return dt
mod = __import__(modname, globals(), locals(), [classname], 0)
if hasattr(mod, classname):
cls_ = getattr(mod, classname)
data = {
k: v
for k, v in d.items() if not k.startswith("@")
}
if hasattr(cls_, "from_dict"):
return cls_.from_dict(data)
elif np is not None and modname == "numpy" and classname == "array":
if d["dtype"].startswith('complex'):
return np.array([
r + i * 1j for r, i in zip(*d["data"])], dtype=d["dtype"])
return np.array(d["data"], dtype=d["dtype"])
elif (bson is not None) and modname == "bson.objectid" and classname == "ObjectId":
return bson.objectid.ObjectId(d["oid"])
return {
self.process_decoded(k): self.process_decoded(v)
for k, v in d.items()
}
if isinstance(d, list):
return [self.process_decoded(x) for x in d]
return d
[docs] def decode(self, s):
"""
Overrides decode from JSONDecoder.
:param s: string
:return: Object.
"""
d = json.JSONDecoder.decode(self, s)
return self.process_decoded(d)
[docs]class MSONError(Exception):
"""
Exception class for serialization errors.
"""
[docs]def jsanitize(obj, strict=False, allow_bson=False):
"""
This method cleans an input json-like object, either a list or a dict or
some sequence, nested or otherwise, by converting all non-string
dictionary keys (such as int and float) to strings, and also recursively
encodes all objects using Monty's as_dict() protocol.
Args:
obj: input json-like object.
strict (bool): This parameters sets the behavior when jsanitize
encounters an object it does not understand. If strict is True,
jsanitize will try to get the as_dict() attribute of the object. If
no such attribute is found, an attribute error will be thrown. If
strict is False, jsanitize will simply call str(object) to convert
the object to a string representation.
allow_bson (bool): This parameters sets the behavior when jsanitize
encounters an bson supported type such as objectid and datetime. If
True, such bson types will be ignored, allowing for proper
insertion into MongoDb databases.
Returns:
Sanitized dict that can be json serialized.
"""
if allow_bson and (isinstance(obj, (datetime.datetime, bytes)) or
(bson is not None
and isinstance(obj, bson.objectid.ObjectId))):
return obj
if isinstance(obj, (list, tuple)):
return [
jsanitize(i, strict=strict, allow_bson=allow_bson) for i in obj
]
if np is not None and isinstance(obj, np.ndarray):
return [
jsanitize(i, strict=strict, allow_bson=allow_bson)
for i in obj.tolist()
]
if isinstance(obj, dict):
return {
k.__str__(): jsanitize(v, strict=strict, allow_bson=allow_bson)
for k, v in obj.items()
}
if isinstance(obj, (int, float)):
return obj
if obj is None:
return None
if not strict:
return obj.__str__()
if isinstance(obj, str):
return obj.__str__()
return jsanitize(obj.as_dict(), strict=strict, allow_bson=allow_bson)