def test_Delay_copyConstructor(self): o1 = libsbml.Delay(2,4) node = libsbml.ASTNode(libsbml.AST_CONSTANT_PI) o1.setMath(node) node = None self.assert_( o1.getMath() != None ) o2 = libsbml.Delay(o1) self.assert_( o2.getMath() != None ) self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() ) o2 = None o1 = None pass
def test_Delay(self):
d = libsbml.Delay(2,4)
self.assertEqual( False, (d.hasRequiredElements()) )
d.setMath(libsbml.parseFormula("a+b"))
self.assertEqual( True, d.hasRequiredElements() )
d = None
pass
def test_Delay_parent_add(self):
d = libsbml.Delay(2, 4)
d.setMath(libsbml.parseFormula("1"))
e = libsbml.Event(2, 4)
e.setDelay(d)
d = None
self.assert_(e == e.getDelay().getParentSBMLObject())
e = None
pass
def test_Event_setDelay2(self):
Delay = libsbml.Delay(2, 1)
Delay.setMath(libsbml.parseFormula("1"))
i = self.E.setDelay(Delay)
self.assert_(i == libsbml.LIBSBML_VERSION_MISMATCH)
self.assertEqual(False, self.E.isSetDelay())
i = self.E.unsetDelay()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
pass
def test_Delay_ancestor_add(self):
d = libsbml.Delay(2,4)
d.setMath(libsbml.parseFormula("1"))
e = libsbml.Event(2,4)
e.setDelay(d)
d = None
obj = e.getDelay()
self.assert_( obj.getAncestorOfType(libsbml.SBML_EVENT) == e )
self.assert_( obj.getAncestorOfType(libsbml.SBML_MODEL) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
e = None
pass
def test_Event_setDelay1(self):
math1 = libsbml.parseFormula("0")
Delay = libsbml.Delay(2, 4)
Delay.setMath(math1)
i = self.E.setDelay(Delay)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(self.E.getDelay() != None)
self.assertEqual(True, self.E.isSetDelay())
i = self.E.unsetDelay()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(False, self.E.isSetDelay())
pass
def test_internal_consistency_check_99905_delay(self): d = libsbml.SBMLDocument(2,4) delay = libsbml.Delay(2,4) e = libsbml.Event(2,4) m = d.createModel() d.setLevelAndVersion(2,2,False) delay.setSBOTerm(5) e.setDelay(delay) m.addEvent(e) errors = d.checkInternalConsistency() self.assert_( errors == 0 ) d = None pass
def test_Event_setDelay(self):
math1 = libsbml.parseFormula("0")
Delay = libsbml.Delay(2,4)
Delay.setMath(math1)
self.E.setDelay(Delay)
self.assert_( self.E.getDelay() != None )
self.assertEqual( True, self.E.isSetDelay() )
if (self.E.getDelay() == Delay):
pass
self.E.setDelay(self.E.getDelay())
self.assert_( self.E.getDelay() != Delay )
self.E.setDelay(None)
self.assertEqual( False, self.E.isSetDelay() )
if (self.E.getDelay() != None):
pass
pass
def test_Delay_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2, 1)
sbmlns.addNamespaces(xmlns)
object = libsbml.Delay(sbmlns)
self.assert_(object.getTypeCode() == libsbml.SBML_DELAY)
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 test_Event_parent_NULL(self):
d = libsbml.SBMLDocument(2, 4)
m = d.createModel()
c = m.createEvent()
ea = c.createEventAssignment()
t = libsbml.Trigger(2, 4)
t.setMath(libsbml.ASTNode())
dy = libsbml.Delay(2, 4)
dy.setMath(libsbml.ASTNode())
c.setTrigger(t)
c.setDelay(dy)
self.assert_(c.getAncestorOfType(libsbml.SBML_MODEL) == m)
self.assert_(c.getTrigger().getParentSBMLObject() == c)
self.assert_(c.getDelay().getSBMLDocument() == d)
self.assert_(ea.getAncestorOfType(libsbml.SBML_EVENT) == c)
c1 = c.clone()
d = None
self.assert_(c1.getAncestorOfType(libsbml.SBML_MODEL) == None)
self.assert_(c1.getParentSBMLObject() == None)
self.assert_(c1.getSBMLDocument() == None)
self.assert_(
c1.getEventAssignment(0).getAncestorOfType(libsbml.SBML_MODEL) ==
None)
self.assert_(
c1.getEventAssignment(0).getAncestorOfType(libsbml.SBML_EVENT) ==
c1)
self.assert_(c1.getEventAssignment(0).getParentSBMLObject() != None)
self.assert_(c1.getEventAssignment(0).getSBMLDocument() == None)
self.assert_(
c1.getTrigger().getAncestorOfType(libsbml.SBML_MODEL) == None)
self.assert_(
c1.getTrigger().getAncestorOfType(libsbml.SBML_EVENT) == c1)
self.assert_(c1.getTrigger().getParentSBMLObject() != None)
self.assert_(c1.getTrigger().getSBMLDocument() == None)
self.assert_(
c1.getDelay().getAncestorOfType(libsbml.SBML_MODEL) == None)
self.assert_(c1.getDelay().getAncestorOfType(libsbml.SBML_EVENT) == c1)
self.assert_(c1.getDelay().getParentSBMLObject() != None)
self.assert_(c1.getDelay().getSBMLDocument() == None)
c1 = None
pass
def setUp(self):
self.D = libsbml.Delay(2, 4)
if (self.D == None):
pass
pass
except Exception, e:
logging.debug(
"SbmlEntityTableModel.setDataEvent(): Can't set the trigger expression %s for event %s. Error: %s" % (
value, event.getId(), e))
elif row == EVENT_ROW.DELAYED:
try:
event.setDelay(bool(value))
except Exception, e:
logging.debug(
"SbmlEntityTableModel.setDataEvent(): Can't set the delay status %s for event %s. Error: %s" % (
value, event.getId(), e))
elif row == EVENT_ROW.DELAYEXPRESSION:
if event.isSetDelay():
delayObject = event.getDelay()
else: # create new delay object
delayObject = libsbml.Delay(2, 4) # level 2 version 4 SBML object
#TODO: has to be created with all needed attributes; ID, name, etc.
delayMath = libsbml.parseFormula(str(value))
delayObject.setMath(delayMath)
self.dataChanged.emit(index, index)
return True
return False
# helper methods
def getReactants(self, reaction):
"""
Returns a string of the reactants of the given Reaction.
def test_Delay(self):
d = libsbml.Delay(2, 4)
self.assertEqual(True, d.hasRequiredAttributes())
d = None
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 test_Delay_constructor(self):
s = None
try:
s = libsbml.Delay(2, 1)
s = libsbml.Delay(2, 2)
s = libsbml.Delay(2, 3)
s = libsbml.Delay(2, 4)
s = libsbml.Delay(3, 1)
s = libsbml.Delay(self.SN21)
s = libsbml.Delay(self.SN22)
s = libsbml.Delay(self.SN23)
s = libsbml.Delay(self.SN24)
s = libsbml.Delay(self.SN31)
except ValueError:
inst = sys.exc_info()[1]
s = None
pass
self.assert_(s != None)
msg = ""
try:
s = libsbml.Delay(1, 1)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.Delay(1, 2)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.Delay(9, 9)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.Delay(self.SN11)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.Delay(self.SN12)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
try:
s = libsbml.Delay(self.SN99)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
