# GillesPy2 is a modeling toolkit for biochemical simulation.
# Copyright (C) 2019-2023 GillesPy2 developers.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import re
import copy
import json
import pydoc
import hashlib
from json import JSONEncoder
import numpy
import gillespy2
[docs]class Jsonify:
"""
Interface to allow for instances of arbitrary types to be encoded into json strings
and decoded into new objects.
"""
_translation_table = None
[docs] def to_json(self, encode_private=True) -> str:
"""
Convert self into a json string.
:param encode_private: If True all private (prefixed of '_') will be encoded. None if False.
:type encode_private: bool
:returns: The JSON representation of self.
"""
encoder = ComplexJsonCoder(encode_private=encode_private)
return json.dumps(copy.deepcopy(self), indent=4, sort_keys=True, default=encoder.default)
[docs] @classmethod
def from_json(cls, json_str: str) -> object:
"""
Convert some json_str into a decoded Python type. This function should
return a new instance of the type.
:param json_str: A json str to be converted into a new type instance.
:type json_str: str
:returns: A decoded object.
"""
# If the json_str is actually a dict, it means we've decoded as much as possible.
if isinstance(json_str, dict):
return cls.from_dict(json_str)
decoder = ComplexJsonCoder()
return json.loads(json_str, object_hook=decoder.decode)
[docs] def to_dict(self) -> dict:
"""
Convert the object into a dictionary ready for json encoding.
Note: Complex types that inherit from Jsonify do not need to be manually encoded.
By default, this function will return a dictionary of the object's public types.
:returns: The backing var dictionary of the object.
"""
return self.__dict__.copy()
[docs] @classmethod
def from_dict(cls, src_dict: dict) -> object:
"""
Convert some dict into a new instance of a python type.
This function will return a __new__ instance of the type.
:param src_dict: The dictionary to apply onto the new instance.
:type src_dict: dict
:returns: A new object with its backing __dict__ set to a copy of src_dict.
"""
new = cls.__new__(cls)
new.__dict__ = src_dict.copy()
return new
[docs] def to_anon(self):
"""
Converts self into an anonymous instance of self.
"""
return self.get_translation_table().obj_to_anon(copy.deepcopy(self))
[docs] def to_named(self):
"""
Converts self into a named instance of self.
"""
return self.get_translation_table().obj_to_named(copy.deepcopy(self))
[docs] def get_translation_table(self) -> "TranslationTable":
"""
Make and/or return the translation table.
:returns: A TranslationTable instance.
"""
if self._translation_table is None:
self._translation_table = self.make_translation_table()
return self._translation_table
[docs] def make_translation_table(self) -> "TranslationTable":
"""
Make a translation table that describes key:value pairs to convert
user-define data into generic equivalents.
:returns: A newly generated TranslationTable instance.
"""
raise NotImplementedError("make_translation_table() has not been implemented.")
[docs] def public_vars(self) -> dict:
"""
Gets a dictionary of public vars that exist on self. Keys starting with '_' are ignored.
:returns: A dictionary containing all public ('_'-prefixed) variables on the object.
"""
return {k: v for k, v in vars(self).items() if not k.startswith("_")}
[docs] def get_json_hash(self, ignore_whitespace=True, hash_private_vals=False) -> str:
"""
Get the hash of the json representation of self.
:param ignore_whitespace: If set to True all whitespace will be stripped from the JSON
prior to being hashed.
:type ignore_whitespace: bool
:param hash_private_vals: If set to True all private and non-private variables will
be included in the hash.
:type hash_private_vals: bool
:returns: An MD5 hash of the object's sorted JSON representation.
"""
# If _hash_private_vars is set, hash ALL properties on the object.
model_json = self.to_json(encode_private=hash_private_vals)
# If ignore_whitespace is set, strip out all whitespace characters.
if ignore_whitespace:
model_json = re.sub(r"\s+", "", model_json)
return hashlib.md5(str.encode(model_json)).hexdigest()
def __eq__(self, obj: "Jsonify"):
"""
Overload to compare the json of two objects that derive from Jsonify.
This method will not do any additional translation.
:param obj: The Jsonify object to compare against.
:type obj: Jsonify
:returns: True if equal, False if not.
"""
return self.get_json_hash() == obj.get_json_hash()
[docs]class ComplexJsonCoder(JSONEncoder):
"""
This class delegates the encoding and decoding of objects to one or more implementees.
:param translation_table: A TranslationTable instance that will be used to
translate objects.
:type translation_table: TranslationTable
:param encode_private: If set to True then all private and public variables will
be converted to JSON. If False, only public.
:type encode_private: bool
"""
def __init__(self, translation_table=None, encode_private=True, **kwargs):
super().__init__(**kwargs)
self._translation_table = translation_table
self._encode_private = encode_private
self._delegation_table = {
numpy.ndarray: NdArrayCoder,
numpy.int64: Int64Coder,
set: SetCoder,
type: TypeCoder
}
[docs] def default(self, o: object):
"""
This function is called when json.dumps() fires. default() is a bad name for the function,
but anything else makes JSONEncoder freak out.
:param o: The object that is currently being encoded into JSON.
"""
# If o is of matching type, use a custom coder.
for obj_type, coder in self._delegation_table.items():
if isinstance(o, obj_type):
return coder.to_dict(o)
if not isinstance(o, Jsonify):
return super().default(o)
if self._encode_private:
model = o.to_dict()
else:
# Strip private variables from the object.
model = {}
for key, val in o.to_dict().items():
if key.startswith("_") and not key.startswith("__"):
continue
model[key] = val
# If the model is some subclass of gillespy2.core.model.Model, then manually set its type.
if issubclass(o.__class__, gillespy2.core.Model):
model["_type"] = f"{gillespy2.core.Model.__module__}.{gillespy2.core.Model.__name__}"
else:
model["_type"] = f"{o.__class__.__module__}.{o.__class__.__name__}"
return model
[docs] def decode(self, json_dict: dict):
"""
Decode the JSON dictionary into a valid Python object.
:param json_dict: The JSON dictionary to decode.
:type json_dict: dict
:returns: The decoded form of the JSON dictionary.
"""
# _type is a field embedded by the encoder to indicate which
# Jsonify instance will be used to decode the json string.
if "_type" not in json_dict:
return json_dict
json_type = pydoc.locate(json_dict["_type"])
if json_type is None:
raise Exception(f"{json_type} does not exist.")
# If the type is not a subclass of Jsonify, throw an exception.
# We do this to prevent the execution of arbitrary code.
if not issubclass(json_type, Jsonify):
raise Exception(f"{json_type}")
return json_type.from_json(json_dict)
[docs]class TranslationTable(Jsonify):
"""
This class contains functions to enable arbitrary object trees to be "translated" to anonymous
and named objects. This behavior is defined by a map of 'named' and 'anon' key values.
:param to_anon: A mapping of 'named' to 'anonymous' strings to be used when converting
user-defined names to anon.
:type to_anon: dict[str, str]
"""
def __init__(self, to_anon: "dict[str, str]"):
self.to_anon = to_anon.copy()
self.to_named = dict((v, k) for k, v in list(self.to_anon.items()))
[docs] def obj_to_anon(self, obj: object):
"""
Recursively anonymise all named properties on the object.
:param obj: The object to anonymize.
:type obj: object
:returns: An anonymized instance of self.
"""
return self.recursive_translate(obj, self.to_anon)
[docs] def obj_to_named(self, obj):
"""
Recursively identify all anonymous properties on the object.
:param obj: The object that will be converted to named.
:type obj: object
:returns: A named instance of self.
"""
return self.recursive_translate(obj, self.to_named)
[docs] def recursive_translate(self, obj: object, translation_table: "dict[str, str]"):
"""
Recursively search through the object tree searching for property value matches in the
translation table. If a match is found, substitute.
:param obj: The object that will be translated.
:type obj: object
:param translation_table: The mapping to translate by.
:type translation_table: TranslationTable
"""
# If a translation table exists on the object, remove and save it.
if "_translation_table" in obj.__dict__:
saved_table = obj.__dict__.pop("_translation_table")
translated = self._recursive_translate(obj, translation_table)
# Restore the original translation table, if needed.
if saved_table is not None:
obj.__dict__["_translation_table"] = saved_table
return translated
def _recursive_translate(self, obj: object, translation_table: "dict[str, str]"):
# The obj is a class if it's an instance of Jsonify. Class property names *cannot*
# be changed, so translate just the values.
if isinstance(obj, Jsonify):
for key in vars(obj).keys():
vars(obj)[key] = self._recursive_translate(vars(obj)[key], translation_table)
elif isinstance(obj, list):
for item in obj:
item = self._recursive_translate(item, translation_table)
elif isinstance(obj, dict):
# Convert the dictionary into a list of tuples.
# This makes it easier to modify key names.
obj = list((k, v) for k, v in obj.items())
new_pairs = [ ]
for pair in obj:
new_pairs.append((
self._recursive_translate(pair[0], translation_table),
self._recursive_translate(pair[1], translation_table)
))
obj = dict((x[0], x[1]) for x in new_pairs)
# If the obj is a string, translate it via a regex replace.
# Note: mathematical functions contain additional characters that should not be translated.
elif isinstance(obj, str):
# To handle functions, grab all complete words from the string.
matches = re.finditer("([0-z])+", obj)
# For each match, translate the group.
for match in matches:
group = match.group()
obj = obj.replace(group, translation_table.get(group, group))
return obj
[docs]class NdArrayCoder(Jsonify):
""" This JSON coder enables support for the `numpy.ndarray` type. """
[docs] @staticmethod
def to_dict(obj):
return {
"data": obj.tolist(),
"_type": f"{NdArrayCoder.__module__}.{NdArrayCoder.__name__}"
}
[docs] @staticmethod
def from_json(obj):
return numpy.array(obj["data"])
[docs]class Int64Coder(Jsonify):
""" This JSON coder enables support for the `numpy.int64` type. """
[docs] @staticmethod
def to_dict(obj):
return {
"data": int(obj),
"_type": f"{Int64Coder.__module__}.{Int64Coder.__name__}"
}
[docs] @staticmethod
def from_json(obj):
return numpy.int64(obj["data"])
[docs]class SetCoder(Jsonify):
""" This JSON coder enables support for the `set` type. """
[docs] @staticmethod
def to_dict(obj):
return {
"data": list(obj),
"_type": f"{SetCoder.__module__}.{SetCoder.__name__}"
}
[docs] @staticmethod
def from_json(obj):
return set(obj["data"])
[docs]class TypeCoder(Jsonify):
""" This JSON coder enables support for the 'type' type. """
[docs] @staticmethod
def to_dict(obj):
return {
"data": type(obj),
"_type": f"{TypeCoder.__module__}.{TypeCoder.__name__}"
}
[docs] @staticmethod
def from_json(obj):
return pydoc.locate(obj["data"])
