cobra.io.web#

Provide functionality to access remote model repositories.

Submodules#

Classes#

`AbstractModelRepository`	Define an abstract base class that describes a remote model repository.
`BiGGModels`	Define a concrete implementation of the BiGG Models repository.
`BioModels`	Define a concrete implementation of the BioModels repository.

Functions#

load_model(→ cobra.core.Model)

Download an SBML model from a remote repository.

Package Contents#

class cobra.io.web.AbstractModelRepository(*, url: httpx.URL | str, **kwargs)[source]#

Bases: abc.ABC

Define an abstract base class that describes a remote model repository.

name#

The name of the remote repository.

Type:: str

_progress#

name: str = 'Abstract'#

_url#

property url: httpx.URL#: Return the repository’s URL.

abstractmethod get_sbml(model_id: str) → bytes[source]#

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

class cobra.io.web.BiGGModels(**kwargs)[source]#

Bases: cobra.io.web.abstract_model_repository.AbstractModelRepository

Define a concrete implementation of the BiGG Models repository.

name#

The name of the BiGG Models repository.

Type:: str

name: str = 'BiGG Models'#

get_sbml(model_id: str) → bytes[source]#

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.

class cobra.io.web.BioModels(**kwargs)[source]#

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[source]#

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.

cobra.io.web.load_model(model_id: str, repositories: Iterable[cobra.io.web.abstract_model_repository.AbstractModelRepository] = DEFAULT_REPOSITORIES, cache: bool = True) → cobra.core.Model[source]#

Download an SBML model from a remote repository.

Downloaded SBML documents are by default stored in a cache on disk such that future access is much faster. By default, models can be loaded from the following repositories:

BiGG Models
BioModels

You can use the AbstractModelRepository class as a parent to implement your own repository accessor which you pass to the load_model function. In case you implement a new interface, please consider submitting a pull request to COBRApy.

Parameters:

model_id (str) – The identifier of the desired metabolic model. This is typically repository specific.
repositories (iterable, optional) – An iterable of repository accessor instances. The model_id is searched in order.

Returns:

A model instance generated from the SBML document.

Return type:

Model

Raises:

RuntimeError – As with any internet connection, there are multiple errors that can occur.

Examples

# Most of the time calling load_model with an identifier should be enough. >>> print(load_model(“e_coli_core”)) e_coli_core >>> print(load_model(“MODEL1510010000”)) MODEL1510010000