def test_Model_getFunctionDefinitionById(self):
fd1 = libsbml.FunctionDefinition(2, 4)
fd2 = libsbml.FunctionDefinition(2, 4)
fd1.setId("sin")
fd2.setId("cos")
fd1.setMath(libsbml.parseFormula("2"))
fd2.setMath(libsbml.parseFormula("2"))
self.M.addFunctionDefinition(fd1)
self.M.addFunctionDefinition(fd2)
self.assert_(self.M.getNumFunctionDefinitions() == 2)
self.assert_(self.M.getFunctionDefinition("sin") != fd1)
self.assert_(self.M.getFunctionDefinition("cos") != fd2)
self.assert_(self.M.getFunctionDefinition("tan") == None)
pass
def test_Model_add_get_FunctionDefinitions(self):
fd1 = libsbml.FunctionDefinition(2, 4)
fd2 = libsbml.FunctionDefinition(2, 4)
fd1.setId("fd1")
fd2.setId("fd2")
fd1.setMath(libsbml.parseFormula("2"))
fd2.setMath(libsbml.parseFormula("2"))
self.M.addFunctionDefinition(fd1)
self.M.addFunctionDefinition(fd2)
self.assert_(self.M.getNumFunctionDefinitions() == 2)
self.assert_(self.M.getFunctionDefinition(0) != fd1)
self.assert_(self.M.getFunctionDefinition(1) != fd2)
self.assert_(self.M.getFunctionDefinition(2) == None)
pass
def test_FunctionDefinition_copyConstructor(self):
o1 = libsbml.FunctionDefinition(2,4)
o1.setId("c")
self.assert_( o1.getId() == "c" )
node = libsbml.ASTNode(libsbml.AST_CONSTANT_PI)
o1.setMath(node)
node = None
self.assert_( o1.getMath() != None )
o2 = libsbml.FunctionDefinition(o1)
self.assert_( o2.getId() == "c" )
self.assert_( o2.getMath() != None )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_FunctionDefinition(self):
fd = libsbml.FunctionDefinition(2, 4)
self.assertEqual(False, (fd.hasRequiredAttributes()))
fd.setId("fd")
self.assertEqual(True, fd.hasRequiredAttributes())
fd = None
pass
def test_FunctionDefinition_createWith(self):
math = libsbml.parseFormula("lambda(x, x^3)")
fd = libsbml.FunctionDefinition(2, 4)
fd.setId("pow3")
fd.setMath(math)
self.assert_(fd.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION)
self.assert_(fd.getMetaId() == "")
self.assert_(fd.getNotes() == None)
self.assert_(fd.getAnnotation() == None)
self.assert_(fd.getName() == "")
math1 = fd.getMath()
self.assert_(math1 != None)
formula = libsbml.formulaToString(math1)
self.assert_(formula != None)
self.assert_(("lambda(x, x^3)" == formula))
self.assert_(fd.getMath() != math)
self.assertEqual(True, fd.isSetMath())
self.assert_(("pow3" == fd.getId()))
self.assertEqual(True, fd.isSetId())
_dummyList = [math]
_dummyList[:] = []
del _dummyList
_dummyList = [fd]
_dummyList[:] = []
del _dummyList
pass
def test_FunctionDefinition(self):
fd = libsbml.FunctionDefinition(2,4)
self.assertEqual( False, (fd.hasRequiredElements()) )
fd.setMath(libsbml.parseFormula("fd"))
self.assertEqual( True, fd.hasRequiredElements() )
fd = None
pass
def test_FunctionDefinition_parent_add(self):
fd = libsbml.FunctionDefinition(2, 4)
m = libsbml.Model(2, 4)
fd.setId("fd")
fd.setMath(libsbml.parseFormula("l"))
m.addFunctionDefinition(fd)
fd = None
lo = m.getListOfFunctionDefinitions()
self.assert_(lo == m.getFunctionDefinition(0).getParentSBMLObject())
self.assert_(m == lo.getParentSBMLObject())
pass
def test_internal_consistency_check_99911_fd(self):
d = libsbml.SBMLDocument(2,4)
m = d.createModel()
fd = libsbml.FunctionDefinition(2,4)
d.setLevelAndVersion(2,1,False)
fd.setId("fd")
fd.setSBOTerm(2)
m.addFunctionDefinition(fd)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_99912(self):
d = libsbml.SBMLDocument(2,4)
fd = libsbml.FunctionDefinition(2,4)
m = d.createModel()
d.setLevelAndVersion(1,2,False)
c = m.createCompartment()
c.setId("cc")
c.setConstant(False)
m.addFunctionDefinition(fd)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_FunctionDefinition_ancestor_add(self):
fd = libsbml.FunctionDefinition(2,4)
m = libsbml.Model(2,4)
fd.setId("fd")
fd.setMath(libsbml.parseFormula("l"))
m.addFunctionDefinition(fd)
fd = None
lo = m.getListOfFunctionDefinitions()
obj = m.getFunctionDefinition(0)
self.assert_( obj.getAncestorOfType(libsbml.SBML_MODEL) == m )
self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_EVENT) == None )
pass
def test_Model_addFunctionDefinition4(self):
m = libsbml.Model(2, 2)
fd = libsbml.FunctionDefinition(2, 2)
fd.setId("fd")
fd.setMath(libsbml.parseFormula("fd"))
fd1 = libsbml.FunctionDefinition(2, 2)
fd1.setId("fd")
fd1.setMath(libsbml.parseFormula("fd"))
i = m.addFunctionDefinition(fd)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(m.getNumFunctionDefinitions() == 1)
i = m.addFunctionDefinition(fd1)
self.assert_(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID)
self.assert_(m.getNumFunctionDefinitions() == 1)
_dummyList = [fd]
_dummyList[:] = []
del _dummyList
_dummyList = [fd1]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_Model_addFunctionDefinition2(self):
m = libsbml.Model(2, 2)
fd = libsbml.FunctionDefinition(2, 1)
fd.setId("fd")
fd.setMath(libsbml.parseFormula("fd"))
i = m.addFunctionDefinition(fd)
self.assert_(i == libsbml.LIBSBML_VERSION_MISMATCH)
self.assert_(m.getNumFunctionDefinitions() == 0)
_dummyList = [fd]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_FunctionDefinition_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,1) sbmlns.addNamespaces(xmlns) object = libsbml.FunctionDefinition(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION ) self.assert_( object.getMetaId() == "" ) self.assert_( object.getNotes() == None ) self.assert_( object.getAnnotation() == None ) self.assert_( object.getLevel() == 2 ) self.assert_( object.getVersion() == 1 ) self.assert_( object.getNamespaces() != None ) self.assert_( object.getNamespaces().getLength() == 2 ) _dummyList = [ object ]; _dummyList[:] = []; del _dummyList pass
def toSBMLString(net):
metaId = 0
try:
m = libsbml.Model(net.id)
except NotImplementedError:
m = libsbml.Model(sbml_level, sbml_version)
m.setId(net.id)
m.setName(net.name)
m.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
for id, fd in list(net.functionDefinitions.items()):
try:
sfd = libsbml.FunctionDefinition(id)
except:
sfd = libsbml.FunctionDefinition(sbml_level, sbml_version)
sfd.setId(id)
sfd.setName(fd.name)
formula = fd.math
formula = formula.replace('**', '^')
formula = 'lambda(%s, %s)' % (','.join(fd.variables), formula)
sfd.setMath(libsbml.parseFormula(formula))
sfd.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addFunctionDefinition(sfd)
for id, c in list(net.compartments.items()):
try:
sc = libsbml.Compartment(id)
except NotImplementedError:
sc = libsbml.Compartment(sbml_level, sbml_version)
sc.setId(id)
sc.setName(c.name)
sc.setConstant(c.is_constant)
sc.setSize(c.initialValue)
sc.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addCompartment(sc)
for id, s in list(net.species.items()):
try:
ss = libsbml.Species(id)
except NotImplementedError:
ss = libsbml.Species(sbml_level, sbml_version)
ss.setId(id)
ss.setName(s.name)
ss.setCompartment(s.compartment)
if s.initialValue is not None and not isinstance(s.initialValue, str):
ss.setInitialConcentration(s.initialValue)
ss.setBoundaryCondition(s.is_boundary_condition)
ss.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addSpecies(ss)
for id, p in list(net.parameters.items()):
try:
sp = libsbml.Parameter(id)
except NotImplementedError:
sp = libsbml.Parameter(sbml_level, sbml_version)
sp.setId(id)
sp.setName(p.name)
if p.initialValue is not None:
sp.setValue(p.initialValue)
sp.setConstant(p.is_constant)
sp.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addParameter(sp)
for id, r in list(net.rateRules.items()):
try:
sr = libsbml.RateRule()
except NotImplementedError:
sr = libsbml.RateRule(sbml_level, sbml_version)
sr.setVariable(id)
formula = r.replace('**', '^')
sr.setMath(libsbml.parseFormula(formula))
sr.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addRule(sr)
for id, r in list(net.assignmentRules.items()):
try:
sr = libsbml.AssignmentRule()
except NotImplementedError:
sr = libsbml.AssignmentRule(sbml_level, sbml_version)
sr.setVariable(id)
formula = r.replace('**', '^')
sr.setMath(libsbml.parseFormula(formula))
sr.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addRule(sr)
for r, r in list(net.algebraicRules.items()):
try:
sr = libsbml.AlgebraicRule()
except NotImplementedError:
sr = libsbml.AlgebraicRule(sbml_level, sbml_version)
formula = r.replace('**', '^')
sr.setMath(libsbml.parseFormula(formula))
sr.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addRule(sr)
for id, rxn in list(net.reactions.items()):
# Need to identify modifiers in kinetic law and add them to
# stoichiometry
kl_vars = ExprManip.extract_vars(rxn.kineticLaw)
species_in_kl = kl_vars.intersection(list(net.species.keys()))
for s in species_in_kl:
if s not in rxn.stoichiometry:
rxn.stoichiometry[s] = 0
try:
srxn = libsbml.Reaction(id)
except NotImplementedError:
srxn = libsbml.Reaction(sbml_level, sbml_version)
srxn.setId(id)
srxn.setName(rxn.name)
# Handle the case where the model was originally read in from an
# SBML file, so that the reactants and products of the Reaction
# object are explicitly set.
if rxn.reactant_stoichiometry != None and \
rxn.product_stoichiometry != None:
for rid, stoich_list in list(rxn.reactant_stoichiometry.items()):
for stoich in stoich_list:
rxn_add_stoich(srxn, rid, -float(stoich), is_product=False)
for rid, stoich_list in list(rxn.product_stoichiometry.items()):
for stoich in stoich_list:
rxn_add_stoich(srxn, rid, stoich, is_product=True)
# Handle the case where the model was created using the SloppyCell
# API, in which case reactants and products are inferred from their
# stoichiometries
else:
for rid, stoich in list(rxn.stoichiometry.items()):
rxn_add_stoich(srxn, rid, stoich)
formula = rxn.kineticLaw.replace('**', '^')
try:
kl = libsbml.KineticLaw(formula)
except NotImplementedError:
kl = libsbml.KineticLaw(sbml_level, sbml_version)
kl.setFormula(formula)
srxn.setKineticLaw(kl)
srxn.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addReaction(srxn)
for id, e in list(net.events.items()):
try:
se = libsbml.Event(id)
except NotImplementedError:
se = libsbml.Event(sbml_level, sbml_version)
se.setId(id)
se.setName(e.name)
formula = e.trigger.replace('**', '^')
formula = formula.replace('and_func(', 'and(')
formula = formula.replace('or_func(', 'or(')
ast = libsbml.parseFormula(formula)
if ast is None:
raise ValueError('Problem parsing event trigger: %s. Problem may '
'be use of relational operators (< and >) rather '
'than libsbml-friendly functions lt and gt.' %
formula)
try:
se.setTrigger(ast)
except TypeError:
try:
trigger = libsbml.Trigger(ast)
except NotImplementedError:
trigger = libsbml.Trigger(sbml_level, sbml_version)
trigger.setMath(ast)
se.setTrigger(trigger)
formula = str(e.delay).replace('**', '^')
try:
se.setDelay(libsbml.parseFormula(formula))
except TypeError:
try:
se.setDelay(libsbml.Delay(libsbml.parseFormula(formula)))
except NotImplementedError:
delay = libsbml.Delay(sbml_level, sbml_version)
delay.setMath(libsbml.parseFormula(formula))
se.setDelay(delay)
for varId, formula in list(e.event_assignments.items()):
try:
sea = libsbml.EventAssignment()
except NotImplementedError:
sea = libsbml.EventAssignment(sbml_level, sbml_version)
sea.setVariable(varId)
formula = str(formula).replace('**', '^')
formula = formula.replace('and_func(', 'and(')
formula = formula.replace('or_func(', 'or(')
ast = libsbml.parseFormula(formula)
replaceTime(ast)
sea.setMath(ast)
se.addEventAssignment(sea)
se.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addEvent(se)
for id, con in list(net.constraints.items()):
try:
scon = libsbml.Constraint()
except NotImplementedError:
scon = libsbml.Constraint(sbml_level, sbml_version)
scon.setId(con.id)
scon.setName(con.name)
formula = con.trigger.replace('**', '^')
ast = libsbml.parseFormula(formula)
if ast is None:
raise ValueError(
'Problem parsing constraint math: %s. Problem may '
'be use of relational operators (< and >) rather '
'than libsbml-friendly functions lt and gt.' % formula)
scon.setMath(ast)
se.setcon('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addConstraint(scon)
d = libsbml.SBMLDocument(sbml_level, sbml_version)
d.setModel(m)
sbmlStr = libsbml.writeSBMLToString(d)
return sbmlStr
def setUp(self):
self.FD = libsbml.FunctionDefinition(2, 4)
if (self.FD == None):
pass
pass
def test_FunctionDefinition_constructor(self):
s = None
try:
s = libsbml.FunctionDefinition(2, 1)
s = libsbml.FunctionDefinition(2, 2)
s = libsbml.FunctionDefinition(2, 3)
s = libsbml.FunctionDefinition(2, 4)
s = libsbml.FunctionDefinition(3, 1)
s = libsbml.FunctionDefinition(self.SN21)
s = libsbml.FunctionDefinition(self.SN22)
s = libsbml.FunctionDefinition(self.SN23)
s = libsbml.FunctionDefinition(self.SN24)
s = libsbml.FunctionDefinition(self.SN31)
except ValueError:
s = None
pass
self.assert_(s != None)
msg = ""
try:
s = libsbml.FunctionDefinition(1, 1)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.FunctionDefinition(1, 2)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.FunctionDefinition(9, 9)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.FunctionDefinition(self.SN11)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.FunctionDefinition(self.SN12)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
try:
s = libsbml.FunctionDefinition(self.SN99)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
