biomodels¶

Utilities for downloading biomodel models.

The downloads go through the shared session of pymetadata, which retries the transient error responses (429, 500, 502, 503, 504) with an exponential backoff and times out after 30 seconds, so a single hiccup of the BioModels service does not fail a download.

download_file ¶

download_file(url, path)

Download a file.

A transient error response is retried, see the module documentation.

Parameters:

Name	Type	Description	Default
`url`	`str`	url to download from	required
`path`	`Path`	file the content is written to	required

Returns:

Type	Description
`Path`	The path the content was written to.

Raises:

Type	Description
`HTTPError`	if the server answered with an error status
`RequestException`	if the server could not be reached

download_biomodel_omex ¶

download_biomodel_omex(biomodel_id, omex_path)

Download omex for biomodel id.

This downloads the latest version of the OMEX from biomodels via the rest service.

:returns: path to omex Raises :class:HTTPError, if one occurred, i.e. if the model does not exist.

download_biomodel_sbml ¶

download_biomodel_sbml(
    biomodel_id, output_dir, output_format="sbml"
)

Download SBML file for biomodel.

Retrieves the archive from biomodels and gets the SBML files from it. Stores the raw SBML files for output_format='sbml' or creates an OMEX archive in case of output_format='omex'.

:param output_format: 'sbml' or 'omex'

:return: list of location strings Raises :class:HTTPError, if one occurred, i.e. if the model does not exist. Raises :class:ValueError, if invalid format string is provided.

query_curated_biomodels ¶

query_curated_biomodels()

Query the identifiers of the curated biomodels.

A transient error response is retried, see the module documentation.

Returns:

Type	Description
`list[str]`	The sorted identifiers of the manually curated models.

Raises:

Type	Description
`HTTPError`	if the server answered with an error status
`RequestException`	if the server could not be reached