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)