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"""Provide functions for loading metabolic models from local package data."""
import importlib.resources
import cobra.data
from .abstract_model_repository import AbstractModelRepository
class Cobrapy(AbstractModelRepository):
"""
Define a concrete implementation of the cobrapy (local package) repository.
Attributes
----------
name : str
The name of the Cobrapy repository.
"""
name: str = "Cobrapy"
def __init__(
self,
**kwargs,
) -> None:
"""
Initialize a local Cobrapy repository interface.
Other Parameters
----------------
kwargs
Passed to the parent constructor in order to enable multiple inheritance.
"""
super().__init__(url="file://", **kwargs)
def get_sbml(self, model_id: str) -> bytes:
"""
Attempt to open an SBML document from the local repository.
Parameters
----------
model_id : str
The identifier of the desired metabolic model. This is typically repository
specific.
Returns
-------
bytes
A gzip-compressed, UTF-8 encoded SBML document.
"""
return (
importlib.resources.files(cobra.data)
.joinpath(f"{model_id}.xml.gz")
.read_bytes()
)
|
