# -*- coding: utf-8 -*-
from __future__ import absolute_import
from six import string_types
from cobra.io.dict import model_from_dict, model_to_dict
try:
import simplejson as json
except ImportError:
import json
[docs]def to_json(model, sort=False, **kwargs):
"""
Return the model as a JSON document.
``kwargs`` are passed on to ``json.dumps``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
Returns
-------
str
String representation of the cobra model as a JSON document.
See Also
--------
save_json_model : Write directly to a file.
json.dumps : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj[u"version"] = JSON_SPEC
return json.dumps(obj, allow_nan=False, **kwargs)
[docs]def from_json(document):
"""
Load a cobra model from a JSON document.
Parameters
----------
document : str
The JSON document representation of a cobra model.
Returns
-------
cobra.Model
The cobra model as represented in the JSON document.
See Also
--------
load_json_model : Load directly from a file.
"""
return model_from_dict(json.loads(document))
[docs]def save_json_model(model, filename, sort=False, pretty=False, **kwargs):
"""
Write the cobra model to a file in JSON format.
``kwargs`` are passed on to ``json.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
filename : str or file-like
File path or descriptor that the JSON representation should be
written to.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
pretty : bool, optional
Whether to format the JSON more compactly (default) or in a more
verbose but easier to read fashion. Can be partially overwritten by the
``kwargs``.
See Also
--------
to_json : Return a string representation.
json.dump : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj[u"version"] = JSON_SPEC
if pretty:
dump_opts = {
"indent": 4,
"separators": (",", ": "),
"sort_keys": True,
"allow_nan": False,
}
else:
dump_opts = {
"indent": 0,
"separators": (",", ":"),
"sort_keys": False,
"allow_nan": False,
}
dump_opts.update(**kwargs)
if isinstance(filename, string_types):
with open(filename, "w") as file_handle:
json.dump(obj, file_handle, **dump_opts)
else:
json.dump(obj, filename, **dump_opts)
[docs]def load_json_model(filename):
"""
Load a cobra model from a file in JSON format.
Parameters
----------
filename : str or file-like
File path or descriptor that contains the JSON document describing the
cobra model.
Returns
-------
cobra.Model
The cobra model as represented in the JSON document.
See Also
--------
from_json : Load from a string.
"""
if isinstance(filename, string_types):
with open(filename, "r") as file_handle:
return model_from_dict(json.load(file_handle))
else:
return model_from_dict(json.load(filename))