sbmlsim.model.model_resources

Model resources.

Interacting with model resources to retrieve models. This currently includes BioModels, but can easily be extended to other models.

Module Contents

Classes

Source

Class for keeping track of the resolved sources.

Functions

is_urn(source)

Check if urn source.

is_http(source)

Check if http source.

model_from_urn(urn)

Get model string from given URN.

model_from_url(url)

Get model string from given URL.

parse_biomodels_mid(text)

Parse biomodel id from string.

model_from_biomodels(mid)

Get SBML string from given BioModels identifier.

Attributes

logger

sbmlsim.model.model_resources.logger[source]
class sbmlsim.model.model_resources.Source[source]

Class for keeping track of the resolved sources.

source: str[source]
path: pathlib.Path | None[source]
content: str | None[source]
is_path()[source]

Check if the source is a Path.

Return type:

bool

is_content()[source]

Check if the source is Content.

Return type:

bool

to_dict()[source]

Convert to dict.

Used for serialization.

Return type:

Dict[str, Optional[str]]

classmethod from_source(source, base_dir=None)[source]

Resolve the source string.

Parameters:

  • source (Union[Source, str, pathlib.Path]) –

  • base_dir (pathlib.Path) –

Return type:

Source

sbmlsim.model.model_resources.is_urn(source)[source]

Check if urn source.

Parameters:

source (str) –

Return type:

bool

sbmlsim.model.model_resources.is_http(source)[source]

Check if http source.

Parameters:

source (str) –

Return type:

bool

sbmlsim.model.model_resources.model_from_urn(urn)[source]

Get model string from given URN.

Parameters:

urn (str) –

Return type:

str

sbmlsim.model.model_resources.model_from_url(url)[source]

Get model string from given URL.

Handles redirects of the download page.

Parameters:

url (str) –

Returns:

Return type:

str

sbmlsim.model.model_resources.parse_biomodels_mid(text)[source]

Parse biomodel id from string.

Parameters:

text (str) –

Return type:

str

sbmlsim.model.model_resources.model_from_biomodels(mid)[source]

Get SBML string from given BioModels identifier.

Parameters:

mid (str) – biomodels id

Returns:

SBML string

Return type:

str