Source code for monty.json

# coding: utf-8
JSON serialization and deserialization utilities.

from __future__ import absolute_import, unicode_literals
import json
import datetime
import six
    from inspect import getfullargspec as getargspec
except ImportError:
    from inspect import getargspec

    import numpy as np
except ImportError:
    np = None

    import bson
except ImportError:
    bson = None

__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2014, The Materials Virtual Lab"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = ""
__date__ = "1/24/14"

[docs]class MSONable(object): """ 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["@module"] = 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. """
[docs] def as_dict(self): """ A JSON serializable dict representation of an object. """ d = {"@module": self.__class__.__module__, "@class": self.__class__.__name__} if hasattr(self, "__init__"): args = getargspec(self.__init__).args 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.") if hasattr(a, "as_dict"): a = a.as_dict() d[c] = a if hasattr(self, "kwargs"): d.update(**self.kwargs) if hasattr(self, "_kwargs"): d.update(**self._kwargs) return d
[docs] def from_dict(cls, d): decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} return cls(**decoded)
[docs] def to_json(self): """ Returns a json string representation of the MSONable object. """ return json.dumps(self, cls=MontyEncoder)
[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): """ 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): return {"@module": "numpy", "@class": "array", "dtype": o.dtype.__str__(), "data": o.tolist()} elif 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__) 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"] 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 k not in ["@module", "@class"]} if hasattr(cls_, "from_dict"): return cls_.from_dict(data) elif np is not None and modname == "numpy" and classname == \ "array": 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()} elif isinstance(d, list): return [self.process_decoded(x) for x in d] return d
[docs] def decode(self, *args, **kwargs): d = json.JSONDecoder.decode(self, *args, **kwargs) return self.process_decoded(d)
[docs]class MSONError(Exception): """ Exception class for serialization errors. """ pass
[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) 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] elif np is not None and isinstance(obj, np.ndarray): return [jsanitize(i, strict=strict, allow_bson=allow_bson) for i in obj.tolist()] elif isinstance(obj, dict): return {k.__str__(): jsanitize(v, strict=strict, allow_bson=allow_bson) for k, v in obj.items()} elif isinstance(obj, (int, float)): return obj elif obj is None: return None else: if not strict: return obj.__str__() else: if isinstance(obj, six.string_types): return obj.__str__() else: return jsanitize(obj.as_dict(), strict=strict, allow_bson=allow_bson)