Export JSON (pysb.export.json)

Module containing a class for exporting a PySB model to JSON

For information on how to use the model exporters, see the documentation for pysb.export.

class pysb.export.json.JsonExporter(model, docstring=None)

A class for returning the JSON for a given PySB model.

Inherits from pysb.export.Exporter, which implements basic functionality for all exporters.

export(include_netgen=False)

Generate the corresponding JSON for the PySB model associated with the exporter.

Parameters:

include_netgen: bool

Include cached network generation data (reactions, species, local function-derived parameters and expressions) if True.

Returns:

string

The JSON output for the model.

class pysb.export.json.PySBJSONEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Encode a PySB model in JSON

This encoder stores the model without caching the reaction network. To also store the reaction network, see PySBJSONWithNetworkEncoder.

Attributes correspond to their PySB equivalents (monomers, parameters, etc.) and are mostly stored verbatim, with the following exceptions.

• MultiStates and the ANY and WILD state values use a special object format

• References to other components are stored using the component name

• Sympy expressions are encoded as strings using the default encoder

The protocol number specifies semantic compatibility of the JSON output. It should be incremented if new features are added which affect how a model is simulated or prevent the new output from being loaded by pysb.importers.json.PySBJSONDecoder(). See that code for documentation on the different protocol versions. This encoder only produces JSON using the highest protocol currently defined; If you need to generate output for an older protocol, use an older version of PySB in which the desired protocol number was still current.

default(o)

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)

class pysb.export.json.PySBJSONWithNetworkEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Encode a PySB model and its reaction network in JSON

This encoder stores the model including the cached reaction network. To encode the model without the reaction network, see PySBJSONEncoder, which also includes implementation details.