schrodinger.models.json module

This is a module that extends Python’s standard builtin json module. It offers the following additional features:

exception schrodinger.models.json.JSONDecodeError

Bases: ValueError

__init__

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.models.json.JSONEncodeError

Bases: ValueError

__init__

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.models.json.AttributableType

Bases: list

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

append(object) → None -- append object to end
clear() → None -- remove all items from L
copy() → list -- a shallow copy of L
count(value) → integer -- return number of occurrences of value
extend(iterable) → None -- extend list by appending elements from the iterable
index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

insert()

L.insert(index, object) – insert object before index

pop([index]) → item -- remove and return item at index (default last).

Raises IndexError if list is empty or index is out of range.

remove(value) → None -- remove first occurrence of value.

Raises ValueError if the value is not present.

reverse()

L.reverse() – reverse IN PLACE

sort(key=None, reverse=False) → None -- stable sort *IN PLACE*
class schrodinger.models.json.JsonableClassMixin

Bases: object

A mixin that aids in making a class Jsonable. Users must define toJsonImplementation(self) and fromJsonImplementation(cls, json_dict). For example:

class Person(JsonableClassMixin, object):

    def __init__(self, full_name, age):
        self.full_name = full_name
        self.age = age

    def toJsonImplementation(self):
        return {'full_name':self.full_name,
                'age':self.age}

    @classmethod
    def fromJsonImplementation(cls, json_dict):
        return cls(json_dict['full_name'], json_dict['age'])

Now dump and dumps can encode Person:

# Encode to a file
abe = Person('Abraham Lincoln', 208)
with open('abe.json', 'w') as out_file:
    json.dump(abe, out_file)

# Encode to a string
abe_json_string = json.dumps(abe)

If you want to decode the json string or file, you’ll have to use loads or load and then feed in the result to your class’ public class method fromJson():

# Loading an object from a json file
with open('abe.json', 'r') as in_file:
    abe_json = json.load(in_file)
    abe = Person.fromJson(abe_json)

# Loading an object from a json string
abe_json = json.loads(abe_json_string)
abe = Person.fromJson(abe_json)
toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
classmethod fromJsonImplementation(json_dict)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file.
Returns:An instance of the derived class.

:rtype : cls

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from.
Returns:An instance of this class.

:rtype : cls

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

__init__

Initialize self. See help(type(self)) for accurate signature.

schrodinger.models.json.adapter(version)

This function is a decorator used to define an adapter function that takes in a json_obj from an older version of a JsonableClassMixin and returns it modified such that it can be read in by the version of the class specified by the version argument (typically the current version at the time the adapter is written).

As a example, imagine we define a simple class:

class Person:
    # mmshare version: 40000
    def __init__(self, full_name):
        self.full_name = full_name

If, in mmshare version 41000, we split full_name into attributes first_name and last_name, we could define an adapter like so:

class Person:
    # mmshare version: 41000
    def __init__(self, first_name, last_name):
        self.first_name = first_name
        self.last_name = last_name

    @json.adapter(version=41000)
    def _JsonAdapter(self, json_dict):
        full_name = json_dict.pop(full_name)
        fname, lname = full_name.split(' ')
        json_dict['first_name'] = fname
        json_dict['last_name'] = lname
        return json_dict

Note

An adapter function only needs to bring the json_dict up-to-date with the class at the time that the adapter is written. The next time the class is changed in a way that breaks json decoding, a new adapter function should be added to the class that takes in the previous adapter’s output and makes it compatible with the current class. In this way the json framework can decode any older version by automatically passing it through the appropriate chain of adapter functions.

Parameters:version (int, str, or list of str or ints) – The data version to which an older json_dict will be adapted (typically the current version when the adapter is writte).
Raises:TypeError – if version is not an int, str, or list
schrodinger.models.json.dumps(obj, **kwargs)

A wrapper that automatically encodes objects derived from JsonableClassMixin.

If obj does not subclass JsonableClassMixin, then this function will behave exactly like the builtin json.dumps.

schrodinger.models.json.dump(obj, fp, **kwargs)

A wrapper that automatically encodes objects derived from JsonableClassMixin.

If obj does not subclass JsonableClassMixin, then this function will behave exactly like the builtin json.dump.

schrodinger.models.json.loads(json_str, DataClass=None, **kwargs)

A wrapper that automatically decodes json strings serialized from JsonableClassMixin objects.

param DataClass:
 The class of the object that was serialized into json_str. This can be optionally specified to save an extra step if the object was serialized using JsonableClassMixin.

If the json string was not an encoded JsonableClassMixin object, this function will behave exactly like the builtin json.loads.

schrodinger.models.json.load(fp, DataClass=None, **kwargs)

A wrapper that automatically decodes json files serialized from JsonableClassMixin objects.

param DataClass:
 The class of the object that was serialized into json_str. This can be optionally specified to save an extra step if the object was serialized using JsonableClassMixin.

If the json file was not an encoded JsonableClassMixin object, this function will behave exactly like the builtin json.load.

class schrodinger.models.json.JsonableEnum(*args, **kwargs)

Bases: schrodinger.models.json._JsonableEnumBase, enum.Enum

An enumeration.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

fromJsonImplementation = <bound method JsonableEnum.fromJsonImplementation of <enum 'JsonableEnum'>>
toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
class schrodinger.models.json.JsonableIntEnum(*args, **kwargs)

Bases: int, schrodinger.models.json.JsonableClassMixin, enum.Enum

An enumeration.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

fromJsonImplementation = <bound method JsonableIntEnum.fromJsonImplementation of <enum 'JsonableIntEnum'>>
toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
class schrodinger.models.json.JsonableSet

Bases: schrodinger.models.json.JsonableClassMixin, set

ENCODING_KEY = '_python_set_'
toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
classmethod fromJsonImplementation(json_list)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file.
Returns:An instance of the derived class.

:rtype : cls

copy()

Return a shallow copy of a set.

__contains__()

x.__contains__(y) <==> y in x.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

add()

Add an element to a set.

This has no effect if the element is already present.

clear()

Remove all elements from this set.

difference()

Return the difference of two or more sets as a new set.

(i.e. all elements that are in this set but not the others.)

difference_update()

Remove all elements of another set from this set.

discard()

Remove an element from a set if it is a member.

If the element is not a member, do nothing.

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from.
Returns:An instance of this class.

:rtype : cls

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

intersection()

Return the intersection of two sets as a new set.

(i.e. all elements that are in both sets.)

intersection_update()

Update a set with the intersection of itself and another.

isdisjoint()

Return True if two sets have a null intersection.

issubset()

Report whether another set contains this set.

issuperset()

Report whether this set contains another set.

pop()

Remove and return an arbitrary set element. Raises KeyError if the set is empty.

remove()

Remove an element from a set; it must be a member.

If the element is not a member, raise a KeyError.

symmetric_difference()

Return the symmetric difference of two sets as a new set.

(i.e. all elements that are in exactly one of the sets.)

symmetric_difference_update()

Update a set with the symmetric difference of itself and another.

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
union()

Return the union of sets as a new set.

(i.e. all elements that are in either set.)

update()

Update a set with the union of itself and others.