1# coding: utf-8 2""" 3JSON serialization and deserialization utilities. 4""" 5 6import os 7import json 8import types 9import datetime 10 11from hashlib import sha1 12from collections import OrderedDict, defaultdict 13from enum import Enum 14 15from importlib import import_module 16 17from inspect import getfullargspec 18from uuid import UUID 19 20try: 21 import numpy as np 22except ImportError: 23 np = None # type: ignore 24 25try: 26 import pandas as pd 27except ImportError: 28 pd = None # type: ignore 29 30try: 31 import pydantic 32except ImportError: 33 pydantic = None # type: ignore 34 35try: 36 import bson 37except ImportError: 38 bson = None 39 40try: 41 from ruamel import yaml 42except ImportError: 43 try: 44 import yaml # type: ignore 45 except ImportError: 46 yaml = None # type: ignore 47 48__version__ = "3.0.0" 49 50 51def _load_redirect(redirect_file): 52 try: 53 with open(redirect_file, "rt") as f: 54 d = yaml.safe_load(f) 55 except IOError: 56 # If we can't find the file 57 # Just use an empty redirect dict 58 return {} 59 60 # Convert the full paths to module/class 61 redirect_dict = defaultdict(dict) 62 for old_path, new_path in d.items(): 63 old_class = old_path.split(".")[-1] 64 old_module = ".".join(old_path.split(".")[:-1]) 65 66 new_class = new_path.split(".")[-1] 67 new_module = ".".join(new_path.split(".")[:-1]) 68 69 redirect_dict[old_module][old_class] = { 70 "@module": new_module, 71 "@class": new_class, 72 } 73 74 return dict(redirect_dict) 75 76 77class MSONable: 78 """ 79 This is a mix-in base class specifying an API for msonable objects. MSON 80 is Monty JSON. Essentially, MSONable objects must implement an as_dict 81 method, which must return a json serializable dict and must also support 82 no arguments (though optional arguments to finetune the output is ok), 83 and a from_dict class method that regenerates the object from the dict 84 generated by the as_dict method. The as_dict method should contain the 85 "@module" and "@class" keys which will allow the MontyEncoder to 86 dynamically deserialize the class. E.g.:: 87 88 d["@module"] = self.__class__.__module__ 89 d["@class"] = self.__class__.__name__ 90 91 A default implementation is provided in MSONable, which automatically 92 determines if the class already contains self.argname or self._argname 93 attributes for every arg. If so, these will be used for serialization in 94 the dict format. Similarly, the default from_dict will deserialization 95 classes of such form. An example is given below:: 96 97 class MSONClass(MSONable): 98 99 def __init__(self, a, b, c, d=1, **kwargs): 100 self.a = a 101 self.b = b 102 self._c = c 103 self._d = d 104 self.kwargs = kwargs 105 106 For such classes, you merely need to inherit from MSONable and you do not 107 need to implement your own as_dict or from_dict protocol. 108 109 New to Monty V2.0.6.... 110 Classes can be redirected to moved implementations by putting in the old 111 fully qualified path and new fully qualified path into .monty.yaml in the 112 home folder 113 114 Example: 115 old_module.old_class: new_module.new_class 116 """ 117 118 REDIRECT = _load_redirect(os.path.join(os.path.expanduser("~"), ".monty.yaml")) 119 120 def as_dict(self) -> dict: 121 """ 122 A JSON serializable dict representation of an object. 123 """ 124 d = {"@module": self.__class__.__module__, "@class": self.__class__.__name__} 125 126 try: 127 parent_module = self.__class__.__module__.split(".", maxsplit=1)[0] 128 module_version = import_module(parent_module).__version__ # type: ignore 129 d["@version"] = "{}".format(module_version) 130 except (AttributeError, ImportError): 131 d["@version"] = None # type: ignore 132 133 spec = getfullargspec(self.__class__.__init__) 134 args = spec.args 135 136 def recursive_as_dict(obj): 137 if isinstance(obj, (list, tuple)): 138 return [recursive_as_dict(it) for it in obj] 139 if isinstance(obj, dict): 140 return {kk: recursive_as_dict(vv) for kk, vv in obj.items()} 141 if hasattr(obj, "as_dict"): 142 return obj.as_dict() 143 return obj 144 145 for c in args: 146 if c != "self": 147 try: 148 a = self.__getattribute__(c) 149 except AttributeError: 150 try: 151 a = self.__getattribute__("_" + c) 152 except AttributeError: 153 raise NotImplementedError( 154 "Unable to automatically determine as_dict " 155 "format from class. MSONAble requires all " 156 "args to be present as either self.argname or " 157 "self._argname, and kwargs to be present under" 158 "a self.kwargs variable to automatically " 159 "determine the dict format. Alternatively, " 160 "you can implement both as_dict and from_dict." 161 ) 162 d[c] = recursive_as_dict(a) 163 if hasattr(self, "kwargs"): 164 # type: ignore 165 d.update(**getattr(self, "kwargs")) # pylint: disable=E1101 166 if spec.varargs is not None and getattr(self, spec.varargs, None) is not None: 167 d.update({spec.varargs: getattr(self, spec.varargs)}) 168 if hasattr(self, "_kwargs"): 169 d.update(**getattr(self, "_kwargs")) # pylint: disable=E1101 170 if isinstance(self, Enum): 171 d.update({"value": self.value}) # pylint: disable=E1101 172 return d 173 174 @classmethod 175 def from_dict(cls, d): 176 """ 177 :param d: Dict representation. 178 :return: MSONable class. 179 """ 180 decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")} 181 return cls(**decoded) 182 183 def to_json(self) -> str: 184 """ 185 Returns a json string representation of the MSONable object. 186 """ 187 return json.dumps(self, cls=MontyEncoder) 188 189 def unsafe_hash(self): 190 """ 191 Returns an hash of the current object. This uses a generic but low 192 performance method of converting the object to a dictionary, flattening 193 any nested keys, and then performing a hash on the resulting object 194 """ 195 196 def flatten(obj, seperator="."): 197 # Flattens a dictionary 198 199 flat_dict = {} 200 for key, value in obj.items(): 201 if isinstance(value, dict): 202 flat_dict.update({seperator.join([key, _key]): _value for _key, _value in flatten(value).items()}) 203 elif isinstance(value, list): 204 list_dict = {"{}{}{}".format(key, seperator, num): item for num, item in enumerate(value)} 205 flat_dict.update(flatten(list_dict)) 206 else: 207 flat_dict[key] = value 208 209 return flat_dict 210 211 ordered_keys = sorted(flatten(jsanitize(self.as_dict())).items(), key=lambda x: x[0]) 212 ordered_keys = [item for item in ordered_keys if "@" not in item[0]] 213 return sha1(json.dumps(OrderedDict(ordered_keys)).encode("utf-8")) 214 215 @classmethod 216 def __get_validators__(cls): 217 """Return validators for use in pydantic""" 218 yield cls.validate_monty 219 220 @classmethod 221 def validate_monty(cls, v): 222 """ 223 pydantic Validator for MSONable pattern 224 """ 225 if isinstance(v, cls): 226 return v 227 if isinstance(v, dict): 228 new_obj = MontyDecoder().process_decoded(v) 229 if isinstance(new_obj, cls): 230 return new_obj 231 232 new_obj = cls(**v) 233 return new_obj 234 235 raise ValueError(f"Must provide {cls.__name__}, the as_dict form, or the proper") 236 237 @classmethod 238 def __modify_schema__(cls, field_schema): 239 """JSON schema for MSONable pattern""" 240 field_schema.update( 241 { 242 "type": "object", 243 "properties": { 244 "@class": {"enum": [cls.__name__], "type": "string"}, 245 "@module": {"enum": [cls.__module__], "type": "string"}, 246 "@version": {"type": "string"}, 247 }, 248 "required": ["@class", "@module"], 249 } 250 ) 251 252 253class MontyEncoder(json.JSONEncoder): 254 """ 255 A Json Encoder which supports the MSONable API, plus adds support for 256 numpy arrays, datetime objects, bson ObjectIds (requires bson). 257 258 Usage:: 259 260 # Add it as a *cls* keyword when using json.dump 261 json.dumps(object, cls=MontyEncoder) 262 """ 263 264 def default(self, o) -> dict: # pylint: disable=E0202 265 """ 266 Overriding default method for JSON encoding. This method does two 267 things: (a) If an object has a to_dict property, return the to_dict 268 output. (b) If the @module and @class keys are not in the to_dict, 269 add them to the output automatically. If the object has no to_dict 270 property, the default Python json encoder default method is called. 271 272 Args: 273 o: Python object. 274 275 Return: 276 Python dict representation. 277 """ 278 if isinstance(o, datetime.datetime): 279 return {"@module": "datetime", "@class": "datetime", "string": o.__str__()} 280 if isinstance(o, UUID): 281 return {"@module": "uuid", "@class": "UUID", "string": o.__str__()} 282 283 if np is not None: 284 if isinstance(o, np.ndarray): 285 if str(o.dtype).startswith("complex"): 286 return { 287 "@module": "numpy", 288 "@class": "array", 289 "dtype": o.dtype.__str__(), 290 "data": [o.real.tolist(), o.imag.tolist()], 291 } 292 return { 293 "@module": "numpy", 294 "@class": "array", 295 "dtype": o.dtype.__str__(), 296 "data": o.tolist(), 297 } 298 if isinstance(o, np.generic): 299 return o.item() 300 301 if pd is not None: 302 if isinstance(o, pd.DataFrame): 303 return { 304 "@module": "pandas", 305 "@class": "DataFrame", 306 "data": o.to_json(default_handler=MontyEncoder().encode), 307 } 308 309 if bson is not None: 310 if isinstance(o, bson.objectid.ObjectId): 311 return {"@module": "bson.objectid", "@class": "ObjectId", "oid": str(o)} 312 313 if callable(o) and not isinstance(o, MSONable): 314 return _serialize_callable(o) 315 316 try: 317 if pydantic is not None and isinstance(o, pydantic.BaseModel): 318 d = o.dict() 319 else: 320 d = o.as_dict() 321 322 if "@module" not in d: 323 d["@module"] = "{}".format(o.__class__.__module__) 324 if "@class" not in d: 325 d["@class"] = "{}".format(o.__class__.__name__) 326 if "@version" not in d: 327 try: 328 parent_module = o.__class__.__module__.split(".")[0] 329 module_version = import_module(parent_module).__version__ # type: ignore 330 d["@version"] = "{}".format(module_version) 331 except (AttributeError, ImportError): 332 d["@version"] = None 333 return d 334 except AttributeError: 335 return json.JSONEncoder.default(self, o) 336 337 338class MontyDecoder(json.JSONDecoder): 339 """ 340 A Json Decoder which supports the MSONable API. By default, the 341 decoder attempts to find a module and name associated with a dict. If 342 found, the decoder will generate a Pymatgen as a priority. If that fails, 343 the original decoded dictionary from the string is returned. Note that 344 nested lists and dicts containing pymatgen object will be decoded correctly 345 as well. 346 347 Usage: 348 349 # Add it as a *cls* keyword when using json.load 350 json.loads(json_string, cls=MontyDecoder) 351 """ 352 353 def process_decoded(self, d): 354 """ 355 Recursive method to support decoding dicts and lists containing 356 pymatgen objects. 357 """ 358 if isinstance(d, dict): 359 if "@module" in d and "@class" in d: 360 modname = d["@module"] 361 classname = d["@class"] 362 if classname in MSONable.REDIRECT.get(modname, {}): 363 modname = MSONable.REDIRECT[modname][classname]["@module"] 364 classname = MSONable.REDIRECT[modname][classname]["@class"] 365 elif "@module" in d and "@callable" in d: 366 modname = d["@module"] 367 objname = d["@callable"] 368 if d.get("@bound", None) is not None: 369 # if the function is bound to an instance or class, first 370 # deserialize the bound object and then remove the object name 371 # from the function name. 372 obj = self.process_decoded(d["@bound"]) 373 objname = objname.split(".")[1:] 374 else: 375 # if the function is not bound to an object, import the 376 # function from the module name 377 obj = __import__(modname, globals(), locals(), [objname], 0) 378 objname = objname.split(".") 379 try: 380 # the function could be nested. e.g., MyClass.NestedClass.function 381 # so iteratively access the nesting 382 for attr in objname: 383 obj = getattr(obj, attr) 384 385 return obj 386 387 except AttributeError: 388 pass 389 else: 390 modname = None 391 classname = None 392 if modname and modname not in ["bson.objectid", "numpy", "pandas"]: 393 if modname == "datetime" and classname == "datetime": 394 try: 395 dt = datetime.datetime.strptime(d["string"], "%Y-%m-%d %H:%M:%S.%f") 396 except ValueError: 397 dt = datetime.datetime.strptime(d["string"], "%Y-%m-%d %H:%M:%S") 398 return dt 399 400 if modname == "uuid" and classname == "UUID": 401 return UUID(d["string"]) 402 403 mod = __import__(modname, globals(), locals(), [classname], 0) 404 if hasattr(mod, classname): 405 cls_ = getattr(mod, classname) 406 data = {k: v for k, v in d.items() if not k.startswith("@")} 407 if hasattr(cls_, "from_dict"): 408 return cls_.from_dict(data) 409 if pydantic is not None and issubclass(cls_, pydantic.BaseModel): 410 return cls_(**data) 411 elif np is not None and modname == "numpy" and classname == "array": 412 if d["dtype"].startswith("complex"): 413 return np.array( 414 [np.array(r) + np.array(i) * 1j for r, i in zip(*d["data"])], 415 dtype=d["dtype"], 416 ) 417 return np.array(d["data"], dtype=d["dtype"]) 418 elif pd is not None and modname == "pandas" and classname == "DataFrame": 419 decoded_data = MontyDecoder().decode(d["data"]) 420 return pd.DataFrame(decoded_data) 421 elif (bson is not None) and modname == "bson.objectid" and classname == "ObjectId": 422 return bson.objectid.ObjectId(d["oid"]) 423 424 return {self.process_decoded(k): self.process_decoded(v) for k, v in d.items()} 425 426 if isinstance(d, list): 427 return [self.process_decoded(x) for x in d] 428 429 return d 430 431 def decode(self, s): 432 """ 433 Overrides decode from JSONDecoder. 434 435 :param s: string 436 :return: Object. 437 """ 438 d = json.JSONDecoder.decode(self, s) 439 return self.process_decoded(d) 440 441 442class MSONError(Exception): 443 """ 444 Exception class for serialization errors. 445 """ 446 447 448def jsanitize(obj, strict=False, allow_bson=False, enum_values=False): 449 """ 450 This method cleans an input json-like object, either a list or a dict or 451 some sequence, nested or otherwise, by converting all non-string 452 dictionary keys (such as int and float) to strings, and also recursively 453 encodes all objects using Monty's as_dict() protocol. 454 455 Args: 456 obj: input json-like object. 457 strict (bool): This parameters sets the behavior when jsanitize 458 encounters an object it does not understand. If strict is True, 459 jsanitize will try to get the as_dict() attribute of the object. If 460 no such attribute is found, an attribute error will be thrown. If 461 strict is False, jsanitize will simply call str(object) to convert 462 the object to a string representation. 463 allow_bson (bool): This parameters sets the behavior when jsanitize 464 encounters an bson supported type such as objectid and datetime. If 465 True, such bson types will be ignored, allowing for proper 466 insertion into MongoDb databases. 467 enum_values (bool): Convert Enums to their values. 468 469 Returns: 470 Sanitized dict that can be json serialized. 471 """ 472 if isinstance(obj, Enum) and enum_values: 473 return obj.value 474 475 if allow_bson and ( 476 isinstance(obj, (datetime.datetime, bytes)) or (bson is not None and isinstance(obj, bson.objectid.ObjectId)) 477 ): 478 return obj 479 if isinstance(obj, (list, tuple)): 480 return [jsanitize(i, strict=strict, allow_bson=allow_bson, enum_values=enum_values) for i in obj] 481 if np is not None and isinstance(obj, np.ndarray): 482 return [jsanitize(i, strict=strict, allow_bson=allow_bson, enum_values=enum_values) for i in obj.tolist()] 483 if np is not None and isinstance(obj, np.generic): 484 return obj.item() 485 if isinstance(obj, dict): 486 return { 487 k.__str__(): jsanitize(v, strict=strict, allow_bson=allow_bson, enum_values=enum_values) 488 for k, v in obj.items() 489 } 490 if isinstance(obj, (int, float)): 491 return obj 492 if obj is None: 493 return None 494 495 if callable(obj) and not isinstance(obj, MSONable): 496 try: 497 return _serialize_callable(obj) 498 except TypeError: 499 pass 500 501 if not strict: 502 return obj.__str__() 503 504 if isinstance(obj, str): 505 return obj.__str__() 506 507 if pydantic is not None and isinstance(obj, pydantic.BaseModel): 508 return jsanitize(MontyEncoder().default(obj), strict=strict, allow_bson=allow_bson, enum_values=enum_values) 509 510 return jsanitize(obj.as_dict(), strict=strict, allow_bson=allow_bson, enum_values=enum_values) 511 512 513def _serialize_callable(o): 514 if isinstance(o, types.BuiltinFunctionType): 515 # don't care about what builtin functions (sum, open, etc) are bound to 516 bound = None 517 else: 518 # bound methods (i.e., instance methods) have a __self__ attribute 519 # that points to the class/module/instance 520 bound = getattr(o, "__self__", None) 521 522 # we are only able to serialize bound methods if the object the method is 523 # bound to is itself serializable 524 if bound is not None: 525 try: 526 bound = MontyEncoder().default(bound) 527 except TypeError: 528 raise TypeError("Only bound methods of classes or MSONable instances are supported.") 529 530 return { 531 "@module": o.__module__, 532 "@callable": getattr(o, "__qualname__", o.__name__), 533 "@bound": bound, 534 } 535