Source code for

"""Provide a concrete implementation of the BioModels repository interface."""

from io import BytesIO

import httpx

from .abstract_model_repository import AbstractModelRepository

[docs]class BiGGModels(AbstractModelRepository): """ Define a concrete implementation of the BiGG Models repository. Attributes ---------- name : str The name of the BiGG Models repository. """
[docs] name: str = "BiGG Models"
def __init__( self, **kwargs, ) -> None: """ Initialize a BiGG Models repository interface. Other Parameters ---------------- kwargs Passed to the parent constructor in order to enable multiple inheritance. """ super().__init__(url="", **kwargs)
[docs] def get_sbml(self, model_id: str) -> bytes: """ Attempt to download an SBML document from the 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. Raises ------ httpx.HTTPError In case there are any connection problems. """ compressed = BytesIO() filename = f"{model_id}.xml.gz" with self._progress, method="GET", url=self._url.join(filename) ) as response: response.raise_for_status() task_id = self._progress.add_task( description="download", total=int(response.headers["Content-Length"]), model_id=model_id, ) for chunk in response.iter_bytes(): compressed.write(chunk) self._progress.update(task_id=task_id, advance=len(chunk)) return