def convert_SBML_Formula_to_ecell_Expression( self, formula, aModel, aLocalParameterList = [], aDenominator = 1.0 ):
'''## =================================================
formula: string or libsbml.ASTNode
'''## =================================================
if isinstance( formula, str ):
if aDenominator != 1.0:
formula = '( 1.0 / %s ) * ( %s )' % ( aDenominator, formula )
preprocessedFormula = formula.replace( '<t>', self.Model.TimeSymbol )
aASTRootNode = libsbml.parseFormula( preprocessedFormula )
elif isinstance( formula, libsbml.ASTNode ):
if aDenominator != 1.0:
aASTRootNode = libsbml.parseFormula( '( 1.0 / %s ) * ( x )' % aDenominator )
aASTRootNode.removeChild( 1 )
aASTRootNode.addChild( formula.deepCopy() )
else:
aASTRootNode = formula
else:
raise Exception,"DEBUG : Formula must be str or libsbml.ASTNode instance."
## dump_tree_construction_of_AST_node( aASTRootNode )
aASTRootNode = preprocess_math_tree( aASTRootNode, aModel.TimeSymbol )
convertedAST = self._convert_SBML_variable_to_ecell_Expression( aASTRootNode, aLocalParameterList )
return postprocess_math_string( libsbml.formulaToString( convertedAST ), aModel.TimeSymbol )
def convert_SBML_Formula_to_ecell_Expression( self, formula, aModel, aLocalParameterList = [], aDenominator = 1.0 ):
'''## =================================================
formula: string or libsbml.ASTNode
'''## =================================================
if isinstance( formula, str ):
if aDenominator != 1.0:
formula = '( 1.0 / %s ) * ( %s )' % ( aDenominator, formula )
preprocessedFormula = formula.replace( '<t>', self.Model.TimeSymbol )
aASTRootNode = libsbml.parseFormula( preprocessedFormula )
elif isinstance( formula, libsbml.ASTNode ):
if aDenominator != 1.0:
aASTRootNode = libsbml.parseFormula( '( 1.0 / %s ) * ( x )' % aDenominator )
aASTRootNode.removeChild( 1 )
aASTRootNode.addChild( formula.deepCopy() )
else:
aASTRootNode = formula
else:
raise Exception,"DEBUG : Formula must be str or libsbml.ASTNode instance."
## dump_tree_construction_of_AST_node( aASTRootNode )
aASTRootNode = preprocess_math_tree( aASTRootNode, aModel.TimeSymbol )
convertedAST = self._convert_SBML_variable_to_ecell_Expression( aASTRootNode, aLocalParameterList )
return postprocess_math_string( libsbml.formulaToString( convertedAST ), aModel.TimeSymbol )
def test_WriteL3SBML_Event_full(self):
expected = wrapString("<event useValuesFromTriggerTime=\"true\">\n" +
" <trigger initialValue=\"true\" persistent=\"false\">\n" +
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" +
" <true/>\n" +
" </math>\n" +
" </trigger>\n" +
" <priority>\n" +
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </math>\n" +
" </priority>\n" +
"</event>")
e = self.D.createModel().createEvent()
e.setUseValuesFromTriggerTime(True)
t = e.createTrigger()
t.setInitialValue(True)
t.setPersistent(False)
math1 = libsbml.parseFormula("true")
t.setMath(math1)
p = e.createPriority()
math2 = libsbml.parseFormula("2")
p.setMath(math2)
self.assertEqual( True, self.equals(expected,e.toSBML()) )
pass
def test_ValidASTNode_Number(self):
n = libsbml.parseFormula("1.2")
self.assertEqual( True, n.isWellFormedASTNode() )
d = libsbml.parseFormula("d")
n.addChild(d)
self.assertEqual( False, (n.isWellFormedASTNode()) )
n = None
pass
def test_ValidASTNode_binary(self):
n = libsbml.ASTNode(libsbml.AST_DIVIDE)
self.assertEqual( False, (n.isWellFormedASTNode()) )
c = libsbml.parseFormula("c")
n.addChild(c)
self.assertEqual( False, (n.isWellFormedASTNode()) )
d = libsbml.parseFormula("d")
n.addChild(d)
self.assertEqual( True, n.isWellFormedASTNode() )
n = None
pass
def test_ValidASTNode_binary(self):
n = libsbml.ASTNode(libsbml.AST_DIVIDE)
self.assertEqual(False, (n.isWellFormedASTNode()))
c = libsbml.parseFormula("c")
n.addChild(c)
self.assertEqual(False, (n.isWellFormedASTNode()))
d = libsbml.parseFormula("d")
n.addChild(d)
self.assertEqual(True, n.isWellFormedASTNode())
n = None
pass
def handleEvents(self, line, name):
# expect an event, or a new context
if (line[0] == "@"):
self.handleNewContext(line, name)
else:
bits = line.split(":")
if (len(bits) != 2):
sys.stderr.write('Error: expected exactly one ":" on ')
sys.stderr.write('line ' + str(self.count) + '\n')
raise ParseError
(event, assignments) = bits
bits = event.split(";")
trigbits = bits[0].split("=")
if (len(trigbits) < 2):
sys.stderr.write('Error: expected a "=" before ":" on ')
sys.stderr.write('line ' + str(self.count) + '\n')
raise ParseError
id = trigbits[0]
trig = "=".join(trigbits[1:])
e = self.m.createEvent()
e.setId(id)
e.setUseValuesFromTriggerTime(True)
trig = self.trigMangle(trig)
triggerMath = libsbml.parseFormula(trig)
self.replaceTime(triggerMath)
trigger = e.createTrigger()
trigger.setPersistent(True)
trigger.setInitialValue(False)
trigger.setMath(triggerMath)
if (len(bits) == 2):
e.setUseValuesFromTriggerTime(False)
delay = e.createDelay()
delayMath = libsbml.parseFormula(bits[1])
delay.setMath(delayMath)
# SPLIT
if (self.mangle >= 230):
asslist = assignments.split(";")
else:
asslist = assignments.split(",")
for ass in asslist:
bits = ass.split("=")
if (len(bits) != 2):
sys.stderr.write(
'Error: expected exactly one "=" in assignment on')
sys.stderr.write('line ' + str(self.count) + '\n')
raise ParseError
(var, math) = bits
ea = self.m.createEventAssignment()
ea.setVariable(var)
ea.setMath(libsbml.parseFormula(math))
if (name != ""):
e.setName(name)
def handleEvents(self,line,name):
# expect an event, or a new context
if (line[0]=="@"):
self.handleNewContext(line,name)
else:
bits=line.split(":")
if (len(bits)!=2):
sys.stderr.write('Error: expected exactly one ":" on ')
sys.stderr.write('line '+str(self.count)+'\n')
raise ParseError
(event,assignments)=bits
bits=event.split(";")
trigbits=bits[0].split("=")
if (len(trigbits)<2):
sys.stderr.write('Error: expected a "=" before ":" on ')
sys.stderr.write('line '+str(self.count)+'\n')
raise ParseError
id=trigbits[0]
trig="=".join(trigbits[1:])
e=self.m.createEvent()
e.setId(id)
e.setUseValuesFromTriggerTime(True)
trig=self.trigMangle(trig)
triggerMath=libsbml.parseFormula(trig)
self.replaceTime(triggerMath)
trigger=e.createTrigger()
trigger.setPersistent(True)
trigger.setInitialValue(False)
trigger.setMath(triggerMath)
if (len(bits)==2):
e.setUseValuesFromTriggerTime(False)
delay=e.createDelay()
delayMath=libsbml.parseFormula(bits[1])
delay.setMath(delayMath)
# SPLIT
if (self.mangle>=230):
asslist=assignments.split(";")
else:
asslist=assignments.split(",")
for ass in asslist:
bits=ass.split("=")
if (len(bits)!=2):
sys.stderr.write('Error: expected exactly one "=" in assignment on')
sys.stderr.write('line '+str(self.count)+'\n')
raise ParseError
(var,math)=bits
ea=self.m.createEventAssignment()
ea.setVariable(var)
ea.setMath(libsbml.parseFormula(math))
if (name!=""):
e.setName(name)
def test_ValidASTNode_root(self):
n = libsbml.ASTNode(libsbml.AST_FUNCTION_ROOT)
self.assertEqual(False, (n.isWellFormedASTNode()))
c = libsbml.parseFormula("c")
n.addChild(c)
self.assertEqual(True, n.isWellFormedASTNode())
d = libsbml.parseFormula("3")
n.addChild(d)
self.assertEqual(True, n.isWellFormedASTNode())
e = libsbml.parseFormula("3")
n.addChild(e)
self.assertEqual(False, (n.isWellFormedASTNode()))
n = None
pass
def test_ValidASTNode_lambda(self):
n = libsbml.ASTNode(libsbml.AST_LAMBDA)
self.assertEqual(False, (n.isWellFormedASTNode()))
c = libsbml.parseFormula("c")
n.addChild(c)
self.assertEqual(True, n.isWellFormedASTNode())
d = libsbml.parseFormula("d")
n.addChild(d)
self.assertEqual(True, n.isWellFormedASTNode())
e = libsbml.parseFormula("e")
n.addChild(e)
self.assertEqual(True, n.isWellFormedASTNode())
n = None
pass
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_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_addRules(self):
r1 = libsbml.AlgebraicRule(2, 4)
r2 = libsbml.AssignmentRule(2, 4)
r3 = libsbml.RateRule(2, 4)
r2.setVariable("r2")
r3.setVariable("r3")
r1.setMath(libsbml.parseFormula("2"))
r2.setMath(libsbml.parseFormula("2"))
r3.setMath(libsbml.parseFormula("2"))
self.M.addRule(r1)
self.M.addRule(r2)
self.M.addRule(r3)
self.assert_(self.M.getNumRules() == 3)
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_Model_addRules(self):
r1 = libsbml.AlgebraicRule(2,4)
r2 = libsbml.AssignmentRule(2,4)
r3 = libsbml.RateRule(2,4)
r2.setVariable( "r2")
r3.setVariable( "r3")
r1.setMath(libsbml.parseFormula("2"))
r2.setMath(libsbml.parseFormula("2"))
r3.setMath(libsbml.parseFormula("2"))
self.M.addRule(r1)
self.M.addRule(r2)
self.M.addRule(r3)
self.assert_( self.M.getNumRules() == 3 )
pass
def test_ValidASTNode_root(self):
n = libsbml.ASTNode(libsbml.AST_FUNCTION_ROOT)
self.assertEqual( False, (n.isWellFormedASTNode()) )
c = libsbml.parseFormula("c")
n.addChild(c)
self.assertEqual( True, n.isWellFormedASTNode() )
d = libsbml.parseFormula("3")
n.addChild(d)
self.assertEqual( True, n.isWellFormedASTNode() )
e = libsbml.parseFormula("3")
n.addChild(e)
self.assertEqual( False, (n.isWellFormedASTNode()) )
n = 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_ValidASTNode_lambda(self):
n = libsbml.ASTNode(libsbml.AST_LAMBDA)
self.assertEqual( False, (n.isWellFormedASTNode()) )
c = libsbml.parseFormula("c")
n.addChild(c)
self.assertEqual( True, n.isWellFormedASTNode() )
d = libsbml.parseFormula("d")
n.addChild(d)
self.assertEqual( True, n.isWellFormedASTNode() )
e = libsbml.parseFormula("e")
n.addChild(e)
self.assertEqual( True, n.isWellFormedASTNode() )
n = None
pass
def test_Trigger(self):
t = libsbml.Trigger(2,4)
self.assertEqual( False, (t.hasRequiredElements()) )
t.setMath(libsbml.parseFormula("ar"))
self.assertEqual( True, t.hasRequiredElements() )
t = None
pass
def test_EventAssignment(self):
ea = libsbml.EventAssignment(2,4)
self.assertEqual( False, (ea.hasRequiredElements()) )
ea.setMath(libsbml.parseFormula("fd"))
self.assertEqual( True, ea.hasRequiredElements() )
ea = None
pass
def test_SBMLConvertStrict_convertNonStrictUnits(self):
d = libsbml.SBMLDocument(2, 4)
m = d.createModel()
c = m.createCompartment()
c.setId("c")
c.setConstant(False)
p = m.createParameter()
p.setId("p")
p.setUnits("mole")
math = libsbml.parseFormula("p")
ar = m.createAssignmentRule()
ar.setVariable("c")
ar.setMath(math)
self.assert_(d.setLevelAndVersion(2, 1, True) == False)
self.assert_(d.getLevel() == 2)
self.assert_(d.getVersion() == 4)
self.assert_(d.setLevelAndVersion(2, 2, True) == False)
self.assert_(d.getLevel() == 2)
self.assert_(d.getVersion() == 4)
self.assert_(d.setLevelAndVersion(2, 3, True) == False)
self.assert_(d.getLevel() == 2)
self.assert_(d.getVersion() == 4)
self.assert_(d.setLevelAndVersion(1, 2, True) == False)
self.assert_(d.getLevel() == 2)
self.assert_(d.getVersion() == 4)
_dummyList = [d]
_dummyList[:] = []
del _dummyList
pass
def main(args):
"""Usage: evaluateCustomMath formula [model containing values]
"""
if len(args) < 2:
print("Usage: evaluateCustomMath formula [model containing values]")
return 1
formula = args[1]
filename = None
if (len(args) > 2):
filename = args[2]
math = libsbml.parseFormula(formula)
if (math == None):
print("Invalid formula, aborting.")
return 1
doc = None
if filename != None:
doc = libsbml.readSBML(filename)
if doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0:
print(
"The models contains errors, please correct them before continuing."
)
doc.printErrors()
return 1
# the following maps a list of ids to their corresponding model values
# this makes it possible to evaluate expressions involving SIds.
libsbml.SBMLTransforms.mapComponentValues(doc.getModel())
else:
# create dummy document
doc = libsbml.SBMLDocument(3, 1)
result = libsbml.SBMLTransforms.evaluateASTNode(math, doc.getModel())
print("{0} = {1}".format(formula, result))
def test_Constraint(self):
c = libsbml.Constraint(2,4)
self.assertEqual( False, (c.hasRequiredElements()) )
c.setMath(libsbml.parseFormula("a+b"))
self.assertEqual( True, c.hasRequiredElements() )
c = None
pass
def test_EventAssignment(self):
ea = libsbml.EventAssignment(2,4)
self.assertEqual( False, (ea.hasRequiredElements()) )
ea.setMath(libsbml.parseFormula("fd"))
self.assertEqual( True, ea.hasRequiredElements() )
ea = None
pass
def test_internal_consistency_check_21226(self):
d = libsbml.SBMLDocument(3,1)
m = d.createModel()
r = m.createEvent()
r.setUseValuesFromTriggerTime(True)
ea = r.createEventAssignment()
ea.setVariable("s")
ast = libsbml.parseFormula("2*x")
ea.setMath(ast)
t = r.createTrigger()
t.setMath(ast)
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 2 )
self.assert_( d.getError(0).getErrorId() == 21226 )
self.assert_( d.getError(1).getErrorId() == 21226 )
t.setPersistent(True)
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 1 )
self.assert_( d.getError(0).getErrorId() == 21226 )
t.setInitialValue(False)
d.getErrorLog().clearLog()
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_InitialAssignment_setMath(self):
math = libsbml.parseFormula("2 * k")
self.IA.setMath(math)
math1 = self.IA.getMath()
self.assert_(math1 != None)
formula = libsbml.formulaToString(math1)
self.assert_(formula != None)
self.assert_(("2 * k" == formula))
self.assert_(self.IA.getMath() != math)
self.assertEqual(True, self.IA.isSetMath())
self.IA.setMath(self.IA.getMath())
math1 = self.IA.getMath()
self.assert_(math1 != None)
formula = libsbml.formulaToString(math1)
self.assert_(formula != None)
self.assert_(("2 * k" == formula))
self.assert_(self.IA.getMath() != math)
self.IA.setMath(None)
self.assertEqual(False, self.IA.isSetMath())
if (self.IA.getMath() != None):
pass
_dummyList = [math]
_dummyList[:] = []
del _dummyList
pass
def test_MathMLFormatter_cn_units(self):
expected = wrapMathMLUnits(" <cn sbml:units=\"mole\"> 1.2 </cn>\n")
self.N = libsbml.parseFormula("1.2")
self.N.setUnits("mole")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_lambda(self):
expected = wrapMathML(" <lambda>\n" +
" <bvar>\n" +
" <ci> x </ci>\n" +
" </bvar>\n" +
" <bvar>\n" +
" <ci> y </ci>\n" +
" </bvar>\n" +
" <apply>\n" +
" <root/>\n" +
" <degree>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </degree>\n" +
" <apply>\n" +
" <plus/>\n" +
" <apply>\n" +
" <power/>\n" +
" <ci> x </ci>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </apply>\n" +
" <apply>\n" +
" <power/>\n" +
" <ci> y </ci>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </apply>\n" +
" </apply>\n" +
" </apply>\n" +
" </lambda>\n")
self.N = libsbml.parseFormula("lambda(x, y, root(2, x^2 + y^2))")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_cn_e_notation_7(self):
expected = wrapMathML(" <cn type=\"e-notation\"> -1 <sep/> -6 </cn>\n"
)
self.N = libsbml.parseFormula("-1e-6")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_cn_e_notation_4(self):
expected = wrapMathML(" <cn type=\"e-notation\"> 6.0221367 <sep/> 23 </cn>\n"
)
self.N = libsbml.parseFormula("6.0221367e+23")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_SBMLConvertStrict_convertNonStrictUnits(self):
d = libsbml.SBMLDocument(2,4)
m = d.createModel()
c = m.createCompartment()
c.setId( "c")
c.setConstant(False)
p = m.createParameter()
p.setId( "p")
p.setUnits( "mole")
math = libsbml.parseFormula("p")
ar = m.createAssignmentRule()
ar.setVariable( "c")
ar.setMath(math)
self.assert_( d.setLevelAndVersion(2,1,True) == False )
self.assert_( d.getLevel() == 2 )
self.assert_( d.getVersion() == 4 )
self.assert_( d.setLevelAndVersion(2,2,True) == False )
self.assert_( d.getLevel() == 2 )
self.assert_( d.getVersion() == 4 )
self.assert_( d.setLevelAndVersion(2,3,True) == False )
self.assert_( d.getLevel() == 2 )
self.assert_( d.getVersion() == 4 )
self.assert_( d.setLevelAndVersion(1,2,True) == False )
self.assert_( d.getLevel() == 2 )
self.assert_( d.getVersion() == 4 )
_dummyList = [ d ]; _dummyList[:] = []; del _dummyList
pass
def test_AlgebraicRule(self):
ar = libsbml.AlgebraicRule(2,4)
self.assertEqual( False, (ar.hasRequiredElements()) )
ar.setMath(libsbml.parseFormula("ar"))
self.assertEqual( True, ar.hasRequiredElements() )
ar = None
pass
def main (args):
"""Usage: evaluateCustomMath formula [model containing values]
"""
if len(args) < 2:
print("Usage: evaluateCustomMath formula [model containing values]")
return 1;
formula = args[1];
filename = None
if (len(args) > 2):
filename = args[2]
math = libsbml.parseFormula(formula);
if (math == None):
print("Invalid formula, aborting.");
return 1;
doc = None;
if filename != None:
doc = libsbml.readSBML(filename);
if doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0:
print("The models contains errors, please correct them before continuing.");
doc.printErrors();
return 1;
# the following maps a list of ids to their corresponding model values
# this makes it possible to evaluate expressions involving SIds.
libsbml.SBMLTransforms.mapComponentValues(doc.getModel());
else:
# create dummy document
doc = libsbml.SBMLDocument(3, 1);
result = libsbml.SBMLTransforms.evaluateASTNode(math, doc.getModel());
print("{0} = {1}".format(formula, result));
def test_AssignmentRule(self):
r = libsbml.AssignmentRule(2,4)
self.assertEqual( False, (r.hasRequiredElements()) )
r.setMath(libsbml.parseFormula("ar"))
self.assertEqual( True, r.hasRequiredElements() )
r = None
pass
def test_MathMLFormatter_cn_e_notation_7(self):
expected = wrapMathML(
" <cn type=\"e-notation\"> -1 <sep/> -6 </cn>\n")
self.N = libsbml.parseFormula("-1e-6")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
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_MathMLFormatter_minus_unary_2(self):
expected = wrapMathML(" <apply>\n" + " <minus/>\n" +
" <ci> a </ci>\n" + " </apply>\n")
self.N = libsbml.parseFormula("-a")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_Constraint(self):
c = libsbml.Constraint(2,4)
self.assertEqual( False, (c.hasRequiredElements()) )
c.setMath(libsbml.parseFormula("a+b"))
self.assertEqual( True, c.hasRequiredElements() )
c = None
pass
def test_AssignmentRule(self):
r = libsbml.AssignmentRule(2,4)
self.assertEqual( False, (r.hasRequiredElements()) )
r.setMath(libsbml.parseFormula("ar"))
self.assertEqual( True, r.hasRequiredElements() )
r = None
pass
def initializeVariableReferenceList(self):
self.theVariableReferenceList = []
formulaString = self.theSBase.getFormula()
anASTNode = libsbml.parseFormula(formulaString)
self.__convertFormulaToExpression(anASTNode)
self.theExpression = libsbml.formulaToString(anASTNode)
# SBML_ASSIGNMENT_RULE or SBML_RATE_RULE
## if self.theSBase.getType() == 1 \
## or self.theSBase.getType() == 2:
if type(self.theSBase) == libsbml.AssignmentRulePtr or type(self.theSBase) == libsbml.RateRulePtr:
variable = self.theSBase.getVariable()
(fullIDString, sbaseType) = self.rootobj.theSBMLIdManager.searchFullIDFromId(variable)
if sbaseType == libsbml.SBML_SPECIES or sbaseType == libsbml.SBML_PARAMETER:
pass
elif sbaseType == libsbml.SBML_COMPARTMENT:
fullID = ecell.ecssupport.createFullID(fullIDString)
systemPath = ecell.ecssupport.createSystemPathFromFullID(fullID)
fullIDString = "Variable:%s:SIZE" % (systemPath)
else:
raise SBMLConvertError, "SBase [%s] is not found" % (variable)
self.__addVariableReference(fullIDString, 1)
def test_Model_addEvent4(self):
m = libsbml.Model(2, 2)
e = libsbml.Event(2, 2)
t = libsbml.Trigger(2, 2)
t.setMath(libsbml.parseFormula("true"))
e.setId("e")
e.setTrigger(t)
e.createEventAssignment()
e1 = libsbml.Event(2, 2)
e1.setId("e")
e1.setTrigger(t)
e1.createEventAssignment()
i = m.addEvent(e)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(m.getNumEvents() == 1)
i = m.addEvent(e1)
self.assert_(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID)
self.assert_(m.getNumEvents() == 1)
_dummyList = [e]
_dummyList[:] = []
del _dummyList
_dummyList = [e1]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_SBMLConvert_convertToL3_stoichiometryMath(self):
d = libsbml.SBMLDocument(2, 1)
m = d.createModel()
c = m.createCompartment()
c.setId("c")
s = m.createSpecies()
s.setId("s")
s.setCompartment("c")
r = m.createReaction()
sr = r.createReactant()
sr.setSpecies("s")
sm = sr.createStoichiometryMath()
ast = libsbml.parseFormula("c*2")
sm.setMath(ast)
self.assert_(m.getNumRules() == 0)
self.assert_(sr.isSetId() == False)
self.assert_(d.setLevelAndVersion(3, 1, False) == True)
m = d.getModel()
r = m.getReaction(0)
sr = r.getReactant(0)
self.assert_(m.getNumRules() == 1)
self.assert_(sr.isSetId() == True)
rule = m.getRule(0)
self.assert_(sr.getId() == rule.getVariable())
_dummyList = [d]
_dummyList[:] = []
del _dummyList
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 rxn_add_stoich(srxn, rid, stoich, is_product=True):
try:
stoich = float(stoich)
if stoich < 0:
sr = srxn.createReactant()
sr.setStoichiometry(-stoich)
elif stoich > 0:
sr = srxn.createProduct()
sr.setStoichiometry(stoich)
elif stoich == 0:
sr = srxn.createModifier()
sr.setSpecies(rid)
except ValueError:
formula = stoich.replace('**', '^')
math_ast = libsbml.parseFormula(formula)
#try:
# smath = libsbml.StoichiometryMath(math_ast)
#except:
# normally this is in an except block but the try above doesn't throw erro
# I am expecting in libSBML 4.0
try:
smath = libsbml.StoichiometryMath(math_ast)
except NotImplementedError:
smath = libsbml.StoichiometryMath(sbml_level, sbml_version)
smath.setMath(math_ast)
if is_product == True:
sr = srxn.createProduct()
else:
sr = srxn.createReactant()
sr.setSpecies(rid)
sr.setStoichiometryMath(smath)
def evaluableMathML(astnode, variables={}, array=False):
""" Create evaluable python string.
"""
# replace variables with provided values
for key, value in variables.iteritems():
astnode.replaceArgument(key, libsbml.parseFormula(str(value)))
# get formula
formula = libsbml.formulaToL3String(astnode)
# <replacements>
# FIXME: these are not exhaustive, but are improved with examples
if array is False:
# scalar
formula = formula.replace("&&", 'and')
formula = formula.replace("||", 'or')
else:
# np.array
formula = formula.replace("max", 'np.max')
formula = formula.replace("min", 'np.min')
formula = formula.replace("sum", 'np.sum')
formula = formula.replace("product", 'np.prod')
return formula
def test_KineticLaw(self):
kl = libsbml.KineticLaw(2,4)
self.assertEqual( False, (kl.hasRequiredElements()) )
kl.setMath(libsbml.parseFormula("kl"))
self.assertEqual( True, kl.hasRequiredElements() )
kl = None
pass
def test_StoichiometryMath(self):
sm = libsbml.StoichiometryMath(2,4)
self.assertEqual( False, (sm.hasRequiredElements()) )
sm.setMath(libsbml.parseFormula("ar"))
self.assertEqual( True, sm.hasRequiredElements() )
sm = None
pass
def test_MathMLFormatter_minus_unary_1(self):
expected = wrapMathML(" <cn type=\"integer\"> -2 </cn>\n"
)
self.N = libsbml.parseFormula("-2")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def handleFunctions(self, line, name):
# expect either a function or a new section
if (line[0] == "@"):
self.handleNewContext(line, name)
else:
bits = line.split("=")
if (len(bits) != 2):
sys.stderr.write('Error: expected "=" on line ')
sys.stderr.write(str(self.count) + '\n')
raise ParseError
(bit, body) = bits
bits = bit.split("(")
if (len(bits) != 2):
sys.stderr.write('Error: expected "(" on function header ')
sys.stderr.write(str(self.count) + '\n')
raise ParseError
(id, args) = bits
if (args[-1] == ")"):
args = args[:-1]
else:
sys.stderr.write('Error: expected ")" on function header ')
sys.stderr.write(str(self.count) + '\n')
raise ParseError
if (len(args.strip()) > 0):
lam = "lambda(" + args + ", " + body + " )"
else:
lam = "lambda( " + body + " )"
value = libsbml.parseFormula(lam)
# self.replaceTime(value)
f = self.m.createFunctionDefinition()
f.setId(id)
f.setMath(value)
def test_SBMLConvert_convertToL3_stoichiometryMath(self):
d = libsbml.SBMLDocument(2,1)
m = d.createModel()
c = m.createCompartment()
c.setId( "c" )
s = m.createSpecies()
s.setId( "s")
s.setCompartment( "c")
r = m.createReaction()
sr = r.createReactant()
sr.setSpecies( "s")
sm = sr.createStoichiometryMath()
ast = libsbml.parseFormula("c*2")
sm.setMath(ast)
self.assert_( m.getNumRules() == 0 )
self.assert_( sr.isSetId() == False )
self.assert_( d.setLevelAndVersion(3,1,False) == True )
m = d.getModel()
r = m.getReaction(0)
sr = r.getReactant(0)
self.assert_( m.getNumRules() == 1 )
self.assert_( sr.isSetId() == True )
rule = m.getRule(0)
self.assert_( sr.getId() == rule.getVariable() )
_dummyList = [ d ]; _dummyList[:] = []; del _dummyList
pass
def test_MathMLFormatter_piecewise(self):
expected = wrapMathML(" <piecewise>\n" +
" <piece>\n" +
" <apply>\n" +
" <minus/>\n" +
" <ci> x </ci>\n" +
" </apply>\n" +
" <apply>\n" +
" <lt/>\n" +
" <ci> x </ci>\n" +
" <cn type=\"integer\"> 0 </cn>\n" +
" </apply>\n" +
" </piece>\n" +
" <piece>\n" +
" <cn type=\"integer\"> 0 </cn>\n" +
" <apply>\n" +
" <eq/>\n" +
" <ci> x </ci>\n" +
" <cn type=\"integer\"> 0 </cn>\n" +
" </apply>\n" +
" </piece>\n" +
" <piece>\n" +
" <ci> x </ci>\n" +
" <apply>\n" +
" <gt/>\n" +
" <ci> x </ci>\n" +
" <cn type=\"integer\"> 0 </cn>\n" +
" </apply>\n" +
" </piece>\n" +
" </piecewise>\n")
f = "piecewise(-x, lt(x, 0), 0, eq(x, 0), x, gt(x, 0))";
self.N = libsbml.parseFormula(f)
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def handleRules(self, line, name):
# expect either a rule or a new section
# changed by lukas: rules are AssignmentRule by default
# "$assign:" and "$rate:" let choose between different kinds of rules
# this requires the assigned species to have atrribute
# constant set to "False"
if (line[0] == "$" and (not re.match("$(?:rate|assign)\:", line))):
self.handleNewContext(line, name)
else:
rule_type = 1 # standard set to assignment rule (1)
if re.match("$rate\:", line):
rule_type = 2 # set to rate rule
elif re.match("$assign\:", line):
rule_type = 1 # set to assignment rule
line = re.sub("\$\w+\:", "",
line) # replace rule declaration if there
bits = line.split("=")
if (len(bits) != 2):
sys.stderr.write('Error: expected "=" on line ')
sys.stderr.write(str(self.count) + '\n')
raise ParseError
(lhs, rhs) = bits
value = libsbml.parseFormula(rhs)
self.replaceTime(value)
if rule_type == 1:
rule = self.m.createAssignmentRule()
elif rule_type == 2:
rule = self.m.createRateRule()
rule.setVariable(lhs)
rule.setMath(value)
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_MathMLFormatter_cn_e_notation_4(self):
expected = wrapMathML(
" <cn type=\"e-notation\"> 6.0221367 <sep/> 23 </cn>\n")
self.N = libsbml.parseFormula("6.0221367e+23")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_KineticLaw_setMath(self):
math = libsbml.parseFormula("k3 / k2")
self.kl.setMath(math)
math1 = self.kl.getMath()
self.assert_(math1 != None)
formula = libsbml.formulaToString(math1)
self.assert_(formula != None)
self.assert_(("k3 / k2" == formula))
self.assert_(self.kl.getMath() != math)
self.assertEqual(True, self.kl.isSetMath())
self.kl.setMath(self.kl.getMath())
math1 = self.kl.getMath()
self.assert_(math1 != None)
formula = libsbml.formulaToString(math1)
self.assert_(formula != None)
self.assert_(("k3 / k2" == formula))
self.assert_(self.kl.getMath() != math)
self.kl.setMath(None)
self.assertEqual(False, self.kl.isSetMath())
if (self.kl.getMath() != None):
pass
_dummyList = [math]
_dummyList[:] = []
del _dummyList
pass
def test_MathMLFormatter_cn_units(self):
expected = wrapMathMLUnits(" <cn sbml:units=\"mole\"> 1.2 </cn>\n")
self.N = libsbml.parseFormula("1.2")
self.N.setUnits("mole")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
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_MathMLFormatter_sin(self):
expected = wrapMathML(" <apply>\n" + " <sin/>\n" +
" <ci> x </ci>\n" + " </apply>\n")
self.N = libsbml.parseFormula("sin(x)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_InitialAssignment(self):
ia = libsbml.InitialAssignment(2,4)
self.assertEqual( False, (ia.hasRequiredElements()) )
ia.setMath(libsbml.parseFormula("ia"))
self.assertEqual( True, ia.hasRequiredElements() )
ia = None
pass