def create(tmp: bool = False) -> None:
"""Create model."""
create_model(
modules=["sbmlutils.examples.fbc1"],
output_dir=EXAMPLE_RESULTS_DIR,
tmp=tmp,
)
def create(tmp: bool = False) -> None:
"""Create model."""
create_model(
modules=["sbmlutils.examples.dallaman.model"],
output_dir=Path(__file__).parent / "results",
tmp=tmp,
units_consistency=False,
)
def create(tmp: bool = False) -> None:
"""Create model."""
create_model(
modules=["sbmlutils.examples.distrib_distributions"],
output_dir=EXAMPLE_RESULTS_DIR,
tmp=tmp,
units_consistency=False,
)
def test_sbml_level_version(level: int, version: int, tmp_path: Path) -> None:
"""Test that the various levels and versions of SBML can be generated."""
md = {
"mid": "level_version",
"compartments": [Compartment(sid="C", value=1.0)],
"species": [
Species(
sid="S1",
initialConcentration=10.0,
compartment="C",
hasOnlySubstanceUnits=False,
boundaryCondition=True,
)
],
"parameters": [Parameter(sid="k1", value=1.0)],
"reactions": [
Reaction(sid="R1", equation="S1 ->", formula=("k1 * S1 * sin(time)", "-"))
],
}
results = create_model(
modules=md,
output_dir=tmp_path,
tmp=False,
units_consistency=False,
sbml_level=level,
sbml_version=version,
)
doc = read_sbml(source=results.sbml_path, validate=False)
assert level == doc.getLevel()
assert version == doc.getVersion()
def test_model_annotation(tmp_path: Path) -> None:
"""Create minimal model and check that annotation is written correctly."""
model_dict = {
"mid":
"example_annotation",
"compartments": [
Compartment(
sid="C",
value=1.0,
sboTerm=SBO_PHYSICAL_COMPARTMENT,
annotations=[
(BQB.IS, "chebi/CHEBI:28061"), # alpha-D-galactose
],
)
],
}
results = create_model(model_dict,
output_dir=tmp_path,
filename="annotation1.xml")
# check annotations
doc: libsbml.SBMLDocument = read_sbml(source=results.sbml_path)
model: libsbml.Model = doc.getModel()
compartment: libsbml.Compartment = model.getCompartment(0)
assert compartment
cvterms: libsbml.CVTermList = compartment.getCVTerms()
assert len(cvterms) == 1
cv: libsbml.CVTerm = cvterms[0]
assert cv.getNumResources() == 1
def create(tmp: bool = False) -> None:
"""Create model."""
output_dir = Path(__file__).parent
create_model(
modules=["sbmlutils.examples.demo.model"],
output_dir=output_dir / "results",
annotations=output_dir / "demo_annotations.xlsx",
tmp=tmp,
)
# without annotations
create_model(
modules=["sbmlutils.examples.demo.model"],
output_dir=output_dir / "results",
mid="{}_{}_{}".format(model.mid, model.version, "no_annotations"),
tmp=tmp,
)
def create(tmp: bool = False) -> FactoryResult:
"""Create model."""
models_dir = Path(__file__).parent
return create_model(
modules=["sbmlutils.examples.tiny_model.model"],
output_dir=models_dir / "results",
annotations=models_dir / "annotations.xlsx",
tmp=tmp,
)
def create(tmp: bool = False) -> None:
"""Create example setting boundaryCondition."""
m1 = {
"mid":
"m1_boundary_condition",
"compartments": [Compartment(sid="C", value=1.0)],
"species": [
Species(
sid="S1",
initialConcentration=10.0,
compartment="C",
hasOnlySubstanceUnits=False,
boundaryCondition=True,
)
],
"parameters": [Parameter(sid="k1", value=1.0)],
"reactions": [
Reaction(sid="R1",
equation="S1 ->",
formula=("k1 * S1 * sin(time)", None))
],
"assignments": [],
}
m2 = m1.copy()
m2["mid"] = "m2_boundary_condition"
m2["assignments"] = [AssignmentRule("S1", 20.0)]
for d in [m1, m2]:
create_model(
modules=d,
output_dir=EXAMPLE_RESULTS_DIR,
tmp=tmp,
units_consistency=False,
)
def test_model_units_metre(unit: UnitType, tmp_path: Path) -> None:
"""Test that length can be set with metre and meter."""
md = {
"mid": "example_model",
"model_units": ModelUnits(length=unit, ),
}
results = create_model(
modules=md,
output_dir=tmp_path,
tmp=False,
sbml_level=3,
sbml_version=1,
validate=False,
)
val_results = validate_sbml(source=results.sbml_path)
assert val_results.all_count == 0
def test_compartment_value(
value: Any, constant: bool, expected: Dict, tmp_path: Path
) -> None:
m1 = {
"mid": "compartment_value",
"compartments": [Compartment(sid="C", value=value, constant=constant)],
}
result = create_model(
modules=m1,
output_dir=tmp_path,
units_consistency=False,
)
doc = read_sbml(source=result.sbml_path)
model = doc.getModel() # type: libsbml.Model
assert model.getNumCompartments() == expected["compartments"]
assert model.getNumInitialAssignments() == expected["initial_assignments"]
assert model.getNumRules() == expected["rules"]