# -*- coding: utf-8 -*-
from __future__ import absolute_import
import io
from ruamel.yaml.compat import StringIO
from ruamel.yaml.main import YAML
from cobra.io.dict import model_from_dict, model_to_dict
[docs]class MyYAML(YAML):
[docs] def dump(self, data, stream=None, **kwargs):
inefficient = False
if stream is None:
inefficient = True
stream = StringIO()
YAML.dump(self, data, stream, **kwargs)
if inefficient:
return stream.getvalue()
[docs]def to_yaml(model, sort=False, **kwargs):
"""
Return the model as a YAML document.
``kwargs`` are passed on to ``yaml.dump``.
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 YAML document.
See Also
--------
save_yaml_model : Write directly to a file.
ruamel.yaml.dump : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj["version"] = YAML_SPEC
return yaml.dump(obj, **kwargs)
[docs]def from_yaml(document):
"""
Load a cobra model from a YAML document.
Parameters
----------
document : str
The YAML document representation of a cobra model.
Returns
-------
cobra.Model
The cobra model as represented in the YAML document.
See Also
--------
load_yaml_model : Load directly from a file.
"""
content = StringIO(document)
return model_from_dict(yaml.load(content))
[docs]def save_yaml_model(model, filename, sort=False, **kwargs):
"""
Write the cobra model to a file in YAML format.
``kwargs`` are passed on to ``yaml.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
filename : str or file-like
File path or descriptor that the YAML representation should be
written to.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
See Also
--------
to_yaml : Return a string representation.
ruamel.yaml.dump : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj["version"] = YAML_SPEC
if isinstance(filename, str):
with io.open(filename, "w") as file_handle:
yaml.dump(obj, file_handle, **kwargs)
else:
yaml.dump(obj, filename, **kwargs)
[docs]def load_yaml_model(filename):
"""
Load a cobra model from a file in YAML format.
Parameters
----------
filename : str or file-like
File path or descriptor that contains the YAML document describing the
cobra model.
Returns
-------
cobra.Model
The cobra model as represented in the YAML document.
See Also
--------
from_yaml : Load from a string.
"""
if isinstance(filename, str):
with io.open(filename, "r") as file_handle:
return model_from_dict(yaml.load(file_handle))
else:
return model_from_dict(yaml.load(filename))