monty.json — monty 4.0.2 documentation

# Source code for monty.json

    # 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)

    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"))

        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

        @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)

        def to_json(self) -> str:
            """
            Returns a json string representation of the MSONable object.
            """
            return json.dumps(self, cls=MontyEncoder)

        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"))

    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)
        """

        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)

    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)
        """

        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

        def decode(self, s):
            """
            Overrides decode from JSONDecoder.

            :param s: string
            :return: Object.
            """
            d = json.JSONDecoder.decode(self, s)
            return self.process_decoded(d)

    class MSONError(Exception):
        """
        Exception class for serialization errors.
        """

    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)