def test_internal_consistency_check_99904_param(self):
d = libsbml.SBMLDocument(2,4)
p = libsbml.Parameter(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("cc")
p.setId("p")
p.setMetaId("mmm")
m.addParameter(p)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_99904_react(self):
d = libsbml.SBMLDocument(2,4)
r = libsbml.Reaction(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("cc")
r.setId("r")
r.setMetaId("mmm")
m.addReaction(r)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_20306(self):
d = libsbml.SBMLDocument(3,1)
m = d.createModel()
fd = m.createFunctionDefinition()
fd.setId("fd")
errors = d.checkInternalConsistency()
self.assert_( errors == 1 )
self.assert_( d.getError(0).getErrorId() == 20306 )
ast = libsbml.parseFormula("lambda(x, 2*x)")
fd.setMath(ast)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_99901(self):
d = libsbml.SBMLDocument(2,4)
c = libsbml.Compartment(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
dim = 2
c.setSpatialDimensions(dim)
c.setId("c")
m.addCompartment(c)
errors = d.checkInternalConsistency()
self.assert_( errors == 1 )
self.assert_( d.getError(0).getErrorId() == 10103 )
d = None
pass
def test_internal_consistency_check_21007(self):
d = libsbml.SBMLDocument(3,1)
m = d.createModel()
r = m.createConstraint()
errors = d.checkInternalConsistency()
self.assert_( errors == 1 )
self.assert_( d.getError(0).getErrorId() == 21007 )
ast = libsbml.parseFormula("lambda(x, 2*x)")
r.setMath(ast)
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_99905_unit(self):
d = libsbml.SBMLDocument(2,4)
u = libsbml.Unit(2,4)
d.setLevelAndVersion(2,2,False)
m = d.createModel()
ud = m.createUnitDefinition()
ud.setId("ud")
u.setKind(libsbml.UNIT_KIND_MOLE)
u.setSBOTerm(9)
ud.addUnit(u)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_SBMLConvert_convertFromL3_persistent(self):
d = libsbml.SBMLDocument(3, 1)
m = d.createModel()
e = m.createEvent()
t = e.createTrigger()
t.setPersistent(False)
self.assert_(d.setLevelAndVersion(1, 1, False) == False)
self.assert_(d.setLevelAndVersion(1, 2, False) == True)
self.assert_(d.setLevelAndVersion(2, 1, False) == True)
self.assert_(d.setLevelAndVersion(2, 2, False) == True)
self.assert_(d.setLevelAndVersion(2, 3, False) == True)
self.assert_(d.setLevelAndVersion(2, 4, False) == True)
self.assert_(d.setLevelAndVersion(3, 1, False) == True)
pass
def test_internal_consistency_check_99904_rule_alg(self):
d = libsbml.SBMLDocument(2,4)
r = libsbml.AlgebraicRule(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("cc")
r.setMetaId("mmm")
r.setFormula("2")
m.addRule(r)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_RDFAnnotation_testMissingMetaId(self):
doc = libsbml.SBMLDocument(3, 1)
model = doc.createModel()
self.assert_(model != None)
model.setId("test1")
term = libsbml.CVTerm(libsbml.MODEL_QUALIFIER)
term.addResource("testResource")
term.setModelQualifierType(libsbml.BQM_IS)
model.setMetaId("t1")
model.addCVTerm(term)
model.setMetaId("")
test = model.toSBML()
self.assert_(test == "<model id=\"test1\"/>")
pass
def test_internal_consistency_check_99903(self):
d = libsbml.SBMLDocument(2,4)
c = libsbml.Compartment(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c.setConstant(True)
c.setId("c")
m.addCompartment(c)
r = m.createAssignmentRule()
r.setVariable("c")
r.setFormula("2*3")
errors = d.checkInternalConsistency()
self.assert_( errors == 3 )
d = None
pass
def test_SBMLConvert_convertToL2v4_DuplicateAnnotations_model(self): d = libsbml.SBMLDocument(2,1) m = d.createModel() annotation = "<rdf/>\n<rdf/>"; i = (m).setAnnotation(annotation) self.assert_( d.getLevel() == 2 ) self.assert_( d.getVersion() == 1 ) self.assert_( (m).getAnnotation().getNumChildren() == 2 ) self.assert_( d.setLevelAndVersion(2,4,True) == True ) self.assert_( d.getLevel() == 2 ) self.assert_( d.getVersion() == 4 ) m = d.getModel() self.assert_( (m).getAnnotation().getNumChildren() == 1 ) _dummyList = [ d ]; _dummyList[:] = []; del _dummyList pass
def test_internal_consistency_check_20805(self):
d = libsbml.SBMLDocument(3,1)
m = d.createModel()
ia = m.createInitialAssignment()
ast = libsbml.parseFormula("lambda(x, 2*x)")
ia.setMath(ast)
errors = d.checkInternalConsistency()
self.assert_( errors == 1 )
self.assert_( d.getError(0).getErrorId() == 20805 )
ia.setSymbol("fd")
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_20908(self):
d = libsbml.SBMLDocument(3,1)
m = d.createModel()
r = m.createAssignmentRule()
ast = libsbml.parseFormula("lambda(x, 2*x)")
r.setMath(ast)
errors = d.checkInternalConsistency()
self.assert_( errors == 1 )
self.assert_( d.getError(0).getErrorId() == 20908 )
r.setVariable("fd")
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_99904_unitdef(self):
d = libsbml.SBMLDocument(2,4)
u = libsbml.UnitDefinition(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("cc")
u.setId("ud")
u.setMetaId("mmm")
u.createUnit()
m.addUnitDefinition(u)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_99911_rule_rate(self):
d = libsbml.SBMLDocument(2,4)
m = d.createModel()
p = m.createParameter()
p.setId("p")
p.setConstant(False)
r = libsbml.RateRule(2,4)
d.setLevelAndVersion(2,1,False)
r.setVariable("p")
r.setSBOTerm(2)
m.addRule(r)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_SBMLConvert_convertToL3_unit(self):
d = libsbml.SBMLDocument(2, 2)
m = d.createModel()
sid = "C"
ud = m.createUnitDefinition()
ud.setId(sid)
u = ud.createUnit()
u.setKind(libsbml.UNIT_KIND_MOLE)
self.assert_(d.setLevelAndVersion(3, 1, False) == True)
u1 = m.getUnitDefinition(0).getUnit(0)
self.assert_(u1.hasRequiredAttributes() == 1)
_dummyList = [d]
_dummyList[:] = []
del _dummyList
pass
def save_model(model, filename):
""" Save a model to an SBML file.
Arguments:
model (Model): model
filename (str): file path
"""
document = sb.SBMLDocument(DEFAULT_SBML_LEVEL, DEFAULT_SBML_VERSION)
sbml_model = document.createModel(model.id)
save_compartments(model, sbml_model)
save_metabolites(model, sbml_model)
save_reactions(model, sbml_model)
writer = sb.SBMLWriter()
writer.writeSBML(document, filename)
def test_SBMLConvert_convertToL2_SBMLDocument(self):
d = libsbml.SBMLDocument(1, 2)
self.assert_(d.setLevelAndVersion(2, 1, False) == True)
self.assert_(d.getLevel() == 2)
self.assert_(d.getVersion() == 1)
self.assert_(d.setLevelAndVersion(2, 2, False) == True)
self.assert_(d.getLevel() == 2)
self.assert_(d.getVersion() == 2)
self.assert_(d.setLevelAndVersion(2, 3, False) == True)
self.assert_(d.getLevel() == 2)
self.assert_(d.getVersion() == 3)
_dummyList = [d]
_dummyList[:] = []
del _dummyList
pass
def test_internal_consistency_check_99904_species(self):
d = libsbml.SBMLDocument(2,4)
s = libsbml.Species(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("c")
s.setCompartment("c")
s.setId("s")
s.setMetaId("mmm")
m.addSpecies(s)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_SBMLConvert_convertToL1_Species_Amount(self): d = libsbml.SBMLDocument(2,1) m = d.createModel() sid = "C"; c = libsbml.Compartment(2,4) s = libsbml.Species(2,4) c.setId(sid) m.addCompartment(c) s.setCompartment(sid) s.setInitialAmount(2.34) m.addSpecies(s) self.assert_( d.setLevelAndVersion(1,2,True) == True ) self.assert_( s.getInitialAmount() == 2.34 ) _dummyList = [ d ]; _dummyList[:] = []; del _dummyList pass
def test_internal_consistency_check_99924(self):
d = libsbml.SBMLDocument(2,4)
u = libsbml.Unit(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("cc")
ud = m.createUnitDefinition()
ud.setId("ud")
u.setKind(libsbml.UNIT_KIND_MOLE)
u.setMultiplier(9)
ud.addUnit(u)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_99915_rate(self):
d = libsbml.SBMLDocument(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("c")
c.setConstant(False)
r = m.createRateRule()
r.setL1TypeCode(libsbml.SBML_SPECIES_CONCENTRATION_RULE)
r.setFormula("2")
r.setVariable("c")
r.setUnits("mmm")
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_SBMLConvert_convertFromL3_conversionFactor(self):
d = libsbml.SBMLDocument(3, 1)
m = d.createModel()
sid = "P"
m.setConversionFactor(sid)
c = m.createParameter()
c.setId(sid)
c.setConstant(True)
self.assert_(d.setLevelAndVersion(1, 1, True) == False)
self.assert_(d.setLevelAndVersion(1, 2, True) == False)
self.assert_(d.setLevelAndVersion(2, 1, True) == False)
self.assert_(d.setLevelAndVersion(2, 2, True) == False)
self.assert_(d.setLevelAndVersion(2, 3, True) == False)
self.assert_(d.setLevelAndVersion(2, 4, True) == False)
self.assert_(d.setLevelAndVersion(3, 1, True) == True)
pass
def simple_sbml_model():
"""Some testmodel"""
document = libsbml.SBMLDocument(3, 1)
model = document.createModel()
model.setTimeUnits("second")
model.setExtentUnits("mole")
model.setSubstanceUnits('mole')
c1 = model.createCompartment()
c1.setId('C1')
model.addCompartment(c1)
s1 = model.createSpecies()
s1.setId('S1')
s1.setCompartment('C1')
model.addSpecies(s1)
return document, model
def test_constant_species_to_parameters():
document = libsbml.SBMLDocument(3, 1)
model = document.createModel()
model.setTimeUnits("second")
model.setExtentUnits("mole")
model.setSubstanceUnits('mole')
s = model.createSpecies()
s.setId('x1')
s.setConstant(True)
s.setInitialConcentration(1.0)
petab.constant_species_to_parameters(model)
assert len(list(model.getListOfParameters())) == 1
assert len(list(model.getListOfSpecies())) == 0
def create_sbml_model(compartment_id="default",
time_units='second',
extent_units='mole',
substance_units='mole',
length_units='metre',
area_units='square_metre',
volume_units='litre',
volume=1e-6,
model_id=None):
'''
Creates an SBML Level 3 Version 2 model with some fixed standard settings.
Returns the SBMLDocument and the Model object as a tuple.
Refer to python-libsbml for more information on SBML API.
'''
document = libsbml.SBMLDocument(3, 2)
model = document.createModel()
if model_id is None:
model_id = 'biocrnpyler_' + str(np.random.randint(1e6))
model.setId(model_id)
model.setName(model_id)
# Define units for area (not used, but keeps COPASI from complaining)
unitdef = model.createUnitDefinition()
unitdef.setId('square_metre')
unit = unitdef.createUnit()
unit.setKind(libsbml.UNIT_KIND_METRE)
unit.setExponent(2)
unit.setScale(0)
unit.setMultiplier(1)
# Set up required units and containers
model.setTimeUnits(time_units) # set model-wide time units
model.setExtentUnits(extent_units) # set model units of extent
model.setSubstanceUnits(substance_units) # set model substance units
model.setLengthUnits(length_units) # area units (never used?)
model.setAreaUnits(area_units) # area units (never used?)
model.setVolumeUnits(volume_units) # default volume unit
# Define the default compartment
compartment = model.createCompartment()
compartment.setId(compartment_id)
compartment.setName(compartment_id)
compartment.setConstant(True) # keep compartment size constant
compartment.setSpatialDimensions(3) # 3 dimensional compartment
compartment.setVolume(volume) # 1 microliter
# Returning document is enough. document.getModel() gives the model, and model.getCompartment(0) gives the compartment.
return document, model
def create_sbml_model(compartment_id="default",
time_units='second',
extent_units='mole',
substance_units='mole',
length_units='metre',
area_units='square_metre',
volume_units='litre',
volume=1e-6,
model_id=None,
**kwargs):
"""Creates an SBML Level 3 Version 2 model with some fixed standard settings.
Refer to python-libsbml for more information on SBML API.
:param compartment_id:
:param time_units:
:param extent_units:
:param substance_units:
:param length_units:
:param area_units:
:param volume_units:
:param volume:
:param model_id:
:return: the SBMLDocument and the Model object as a tuple
"""
document = libsbml.SBMLDocument(3, 2)
model = document.createModel()
if model_id is None:
model_id = 'biocrnpyler_' + str(randint(1, 1e6))
model.setId(model_id)
model.setName(model_id)
# Define units for area (not used, but keeps COPASI from complaining)
unitdef = model.createUnitDefinition()
unitdef.setId('square_metre')
unit = unitdef.createUnit()
unit.setKind(libsbml.UNIT_KIND_METRE)
unit.setExponent(2)
unit.setScale(0)
unit.setMultiplier(1)
# Set up required units and containers
model.setTimeUnits(time_units) # set model-wide time units
model.setExtentUnits(extent_units) # set model units of extent
model.setSubstanceUnits(substance_units) # set model substance units
model.setLengthUnits(length_units) # area units (never used?)
model.setAreaUnits(area_units) # area units (never used?)
model.setVolumeUnits(volume_units) # default volume unit
return document, model
def template_doc_update(model_id):
""" Create template update model.
:param model_id: model identifier
:return: SBMLDocument
"""
sbmlns = libsbml.SBMLNamespaces(SBML_LEVEL, SBML_VERSION, 'comp',
SBML_COMP_VERSION)
doc = libsbml.SBMLDocument(sbmlns)
doc.setPackageRequired(SBML_COMP_NAME, True)
# model
model = doc.createModel()
model.setId("{}_update".format(model_id))
model.setName("{} (UPDATE)".format(model_id))
model.setSBOTerm(comp.SBO_CONTINOUS_FRAMEWORK)
return doc
def test_event() -> None:
objects = [
Parameter(sid="p1", value=0.0, constant=False),
Event(sid="e1", trigger="time >= 10", assignments={"p1": 10.0}),
]
doc = libsbml.SBMLDocument(3, 1)
model = doc.createModel()
factory.create_objects(model, obj_iter=objects)
events = model.getListOfEvents()
assert len(events) == 1
e = model.getEvent("e1")
assert e is not None
assert e.getId() == "e1"
assignments = e.getListOfEventAssignments()
assert len(assignments) == 1
def test_internal_consistency_check_20623(self):
d = libsbml.SBMLDocument(3,1)
m = d.createModel()
c = m.createCompartment()
c.setId("c")
c.setConstant(True)
s = m.createSpecies()
errors = d.checkInternalConsistency()
self.assert_( errors == 5 )
self.assert_( d.getError(0).getErrorId() == 20623 )
self.assert_( d.getError(1).getErrorId() == 20614 )
self.assert_( d.getError(2).getErrorId() == 20623 )
self.assert_( d.getError(3).getErrorId() == 20623 )
self.assert_( d.getError(4).getErrorId() == 20623 )
s.setId("s")
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 4 )
self.assert_( d.getError(0).getErrorId() == 20614 )
self.assert_( d.getError(1).getErrorId() == 20623 )
self.assert_( d.getError(2).getErrorId() == 20623 )
self.assert_( d.getError(3).getErrorId() == 20623 )
s.setCompartment("c")
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 3 )
self.assert_( d.getError(0).getErrorId() == 20623 )
self.assert_( d.getError(1).getErrorId() == 20623 )
self.assert_( d.getError(2).getErrorId() == 20623 )
s.setHasOnlySubstanceUnits(True)
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 2 )
self.assert_( d.getError(0).getErrorId() == 20623 )
self.assert_( d.getError(1).getErrorId() == 20623 )
s.setBoundaryCondition(True)
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 1 )
self.assert_( d.getError(0).getErrorId() == 20623 )
s.setConstant(True)
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
