biomodels.cases¶

Case construction for a BioModels model.

Every curated model runs the same generic timecourse: there are no expected results (Case.expected is None, the roadrunner simulation of the original SBML becomes the expected results the later stages are compared with, see sbml2cellml.testsuite.runner).

constructs ¶

constructs(model, text)

SBML constructs a model uses, as component tags of a Case.

Parameters:

Name	Type	Description	Default
`model`	`Model`	the model to inspect.	required
`text`	`str`	the file content the model was read from, used to detect a `csymbol` delay (not exposed on the `libsbml.Model` API).	required

Returns:

Type	Description
`str`	The construct tags present in the model, e.g. `("Reactions",
`...`	"AssignmentRules")`.

biomodel_case ¶

biomodel_case(info, sbml_path, packages)

Build the generic timecourse case of a BioModels model.

Parameters:

Name	Type	Description	Default
`info`	`ModelInfo`	metadata of the model.	required
`sbml_path`	`Path`	path of the downloaded SBML file.	required
`packages`	`tuple[str, ...]`	SBML packages the model uses (`models.packages`); each becomes a `<package>:package` component tag so `skip_reason` skips the case the same way it skips a test suite case using an unsupported package.	required

Returns:

Type	Description
`Case`	The case, with `expected=None` and `test_type="TimeCourse"`.
`Case`	`settings.variables` is the species ids, followed by the ids of the
`Case`	rate-rule and assignment-rule targets which are not species
`Case`	(parameters and compartments), in document order and without
`Case`	duplicates; `amount` and `concentration` stay species only.

Raises:

Type	Description
`BioModelsError`	if the SBML file has no model.