cobra.io.web.biomodels_repository

Provide functions for loading metabolic models over the wire.

Classes

BioModelsFile	Define a single BioModels file description.
BioModelsFilesResponse	Define the BioModels files JSON response.
BioModels	Define a concrete implementation of the BioModels repository.

Module Contents

class cobra.io.web.biomodels_repository.BioModelsFile(/, **data: Any)

Bases: pydantic.BaseModel

Define a single BioModels file description.

name: str

size: int = None

class cobra.io.web.biomodels_repository.BioModelsFilesResponse(/, **data: Any)

Bases: pydantic.BaseModel

Define the BioModels files JSON response.

main: List[BioModelsFile] = []

class cobra.io.web.biomodels_repository.BioModels(**kwargs)

Bases: cobra.io.web.abstract_model_repository.AbstractModelRepository

Define a concrete implementation of the BioModels repository.

name

The name of the BioModels repository.

Type:

str

name: str = 'BioModels'

get_sbml(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:

A gzip-compressed, UTF-8 encoded SBML document.

Return type:

bytes

Raises:

• httpx.HTTPError – In case there are any connection problems.

• RuntimeError – If the model’s file listing contains no SBML document, for example when the model is only deposited as a COMBINE (OMEX) archive.