def test_element_invalid_mathml(self):
invalid = wrapMathML(
"<lambda definitionURL=\"http://biomodels.net/SBO/#SBO:0000065\">"
+ "<bvar>" + "<ci>c</ci>" + "</bvar>" + "<apply>" +
" <ci>c</ci>" + "</apply>" + "</lambda>\n")
self.N = libsbml.readMathMLFromString(None)
self.assert_(self.N == None)
self.N = libsbml.readMathMLFromString(invalid)
self.assert_(self.N == None)
pass
def test_element_invalid_mathml(self):
invalid = wrapMathML("<lambda definitionURL=\"http://biomodels.net/SBO/#SBO:0000065\">" +
"<bvar>" +
"<ci>c</ci>" +
"</bvar>" +
"<apply>" +
" <ci>c</ci>" +
"</apply>" +
"</lambda>\n")
self.N = libsbml.readMathMLFromString(None)
self.assert_( self.N == None )
self.N = libsbml.readMathMLFromString(invalid)
self.assert_( self.N == None )
pass
def test_element_ceiling(self):
s = wrapMathML("<apply><ceiling/><cn> 1.6 </cn></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("ceil(1.6)" == self.F))
pass
def cmathml_to_astnode(cmathml: str) -> libsbml.ASTNode:
"""Convert Content MathML string to ASTNode.
:param cmathml: SBML Content MathML string
:return: libsbml.ASTNode
"""
return libsbml.readMathMLFromString(cmathml)
def test_element_neq(self):
s = wrapMathML("<apply> <neq/> <notanumber/> <notanumber/> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("neq(NaN, NaN)" == self.F))
pass
def test_element_not(self):
s = wrapMathML("<apply> <not/> <ci> TooShabby </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("not(TooShabby)" == self.F))
pass
def test_element_math(self):
s = wrapXML("<math xmlns='http://www.w3.org/1998/Math/MathML'/>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_UNKNOWN )
pass
def test_element_factorial(self):
s = wrapMathML("<apply><factorial/><cn> 5 </cn></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "factorial(5)" == self.F ))
pass
def test_element_not(self):
s = wrapMathML("<apply> <not/> <ci> TooShabby </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "not(TooShabby)" == self.F ))
pass
def test_element_ceiling(self):
s = wrapMathML("<apply><ceiling/><cn> 1.6 </cn></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "ceil(1.6)" == self.F ))
pass
def test_element_floor(self):
s = wrapMathML("<apply><floor/><cn> 1.2 </cn></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "floor(1.2)" == self.F ))
pass
def test_element_tanh(self):
s = wrapMathML("<apply><tanh/><ci> x </ci></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("tanh(x)" == self.F))
pass
def test_element_constants_true(self):
s = wrapMathML("<true/>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_CONSTANT_TRUE)
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_power(self):
s = wrapMathML("<apply><power/> <ci>x</ci> <cn>3</cn> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "pow(x, 3)" == self.F ))
pass
def test_element_constants_true(self):
s = wrapMathML("<true/>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_CONSTANT_TRUE )
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_root_2(self):
s = wrapMathML("<apply> <root/> <ci> a </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("sqrt(a)" == self.F))
pass
def test_element_power(self):
s = wrapMathML("<apply><power/> <ci>x</ci> <cn>3</cn> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("pow(x, 3)" == self.F))
pass
def test_element_function_call_1(self):
s = wrapMathML("<apply> <ci> foo </ci> <ci> x </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "foo(x)" == self.F ))
pass
def test_element_root_2(self):
s = wrapMathML("<apply> <root/> <ci> a </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "sqrt(a)" == self.F ))
pass
def test_element_tanh(self):
s = wrapMathML("<apply><tanh/><ci> x </ci></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "tanh(x)" == self.F ))
pass
def __set_kinetic_law(self, reaction, function_definition, parameters):
'''Sets kineticLaw element to reaction.'''
mathml = '<?xml version="1.0" encoding="UTF-8"?>'
mathml += '<math xmlns="http://www.w3.org/1998/Math/MathML">'
mathml += '<apply>'
mathml += '<ci>' + function_definition.getId() + '</ci>'
for parameter in parameters:
mathml += '<ci>' + parameter[2] + '</ci>'
mathml += '</apply>'
mathml += '</math>'
kinetic_law = reaction.createKineticLaw()
kinetic_law.setMath(libsbml.readMathMLFromString(mathml))
for parameter in parameters:
sbo_term = parameter[1]
if sbo_term != sbml_utils.SBO_TERMS[sbml_utils.CONC] and \
sbo_term != sbml_utils.SBO_TERMS[sbml_utils.VOLUME]:
param = kinetic_law.createParameter()
param.setId(parameter[2])
param.setValue(sbml_utils.SBO_TERM_DEFAULT[sbo_term])
param.setUnits(self.__units[sbo_term])
param.setSBOTerm(sbo_term)
return kinetic_law
def test_element_function_call_1(self):
s = wrapMathML("<apply> <ci> foo </ci> <ci> x </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("foo(x)" == self.F))
pass
def test_element_floor(self):
s = wrapMathML("<apply><floor/><cn> 1.2 </cn></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("floor(1.2)" == self.F))
pass
def test_element_factorial(self):
s = wrapMathML("<apply><factorial/><cn> 5 </cn></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("factorial(5)" == self.F))
pass
def test_element_constants_infinity(self):
s = wrapMathML("<infinity/>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_REAL)
self.assert_(util_isInf(self.N.getReal()) == True)
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_operator_times(self):
s = wrapMathML(
"<apply> <times/> <ci> x </ci> <ci> y </ci> <ci> z </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("x * y * z" == self.F))
pass
def test_element_operator_plus(self):
s = wrapMathML(
"<apply> <plus/> <cn> 1 </cn> <cn> 2 </cn> <cn> 3 </cn> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("1 + 2 + 3" == self.F))
pass
def test_element_constants_notanumber(self):
s = wrapMathML("<notanumber/>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_REAL)
self.assertEqual(True, isnan(self.N.getReal()))
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_leq(self):
s = wrapMathML(
"<apply> <leq/> <cn>0</cn> <ci>x</ci> <cn>1</cn> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("leq(0, x, 1)" == self.F))
pass
def test_element_eq(self):
s = wrapMathML(
"<apply> <eq/> <ci>a</ci> <ci>b</ci> <ci>c</ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("eq(a, b, c)" == self.F))
pass
def test_element_cn_integer(self):
s = wrapMathML("<cn type='integer'> 12345 </cn>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_INTEGER )
self.assert_( self.N.getInteger() == 12345 )
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_cn_real(self):
s = wrapMathML("<cn type='real'> 12345.7 </cn>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_REAL)
self.assert_(self.N.getReal() == 12345.7)
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_ci_surrounding_spaces_bug(self):
s = wrapMathML(" <ci> s </ci> ")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_NAME )
self.assert_(( "s" == self.N.getName() ))
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_constants_infinity(self):
s = wrapMathML("<infinity/>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_REAL )
self.assert_( util_isInf(self.N.getReal()) == True )
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_cn_real(self):
s = wrapMathML("<cn type='real'> 12345.7 </cn>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_REAL )
self.assert_( self.N.getReal() == 12345.7 )
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_cn_integer(self):
s = wrapMathML("<cn type='integer'> 12345 </cn>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_INTEGER)
self.assert_(self.N.getInteger() == 12345)
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_constants_notanumber(self):
s = wrapMathML("<notanumber/>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_REAL )
self.assertEqual( True, isnan(self.N.getReal()) )
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_csymbol_delay_1(self):
s = wrapMathML("<csymbol encoding='text' " + "definitionURL='http://www.sbml.org/sbml/symbols/delay'> delay </csymbol>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_FUNCTION_DELAY )
self.assert_(( "delay" == self.N.getName() ))
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_csymbol_avogadro(self):
s = wrapMathML("<csymbol encoding='text' " + "definitionURL='http://www.sbml.org/sbml/symbols/avogadro'> NA </csymbol>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_NAME_AVOGADRO )
self.assert_(( "NA" == self.N.getName() ))
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_ci_surrounding_spaces_bug(self):
s = wrapMathML(" <ci> s </ci> ")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_NAME)
self.assert_(("s" == self.N.getName()))
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_csymbol_time(self):
s = wrapMathML("<csymbol encoding='text' " + "definitionURL='http://www.sbml.org/sbml/symbols/time'> t </csymbol>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_NAME_TIME )
self.assert_(( "t" == self.N.getName() ))
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_ci(self):
s = wrapMathML("<ci> x </ci>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.assert_( self.N.getType() == libsbml.AST_NAME )
self.assert_(( "x" == self.N.getName() ))
self.assert_( self.N.getNumChildren() == 0 )
pass
def test_element_xor(self):
s = wrapMathML("<apply> <xor/> <ci>a</ci> <ci>b</ci> <ci>b</ci> <ci>a</ci> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "xor(a, b, b, a)" == self.F ))
pass
def test_element_neq(self):
s = wrapMathML("<apply> <neq/> <notanumber/> <notanumber/> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "neq(NaN, NaN)" == self.F ))
pass
def test_element_ci(self):
s = wrapMathML("<ci> x </ci>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_NAME)
self.assert_(("x" == self.N.getName()))
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_operator_times(self):
s = wrapMathML("<apply> <times/> <ci> x </ci> <ci> y </ci> <ci> z </ci> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "x * y * z" == self.F ))
pass
def test_element_leq(self):
s = wrapMathML("<apply> <leq/> <cn>0</cn> <ci>x</ci> <cn>1</cn> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "leq(0, x, 1)" == self.F ))
pass
def test_element_operator_plus(self):
s = wrapMathML("<apply> <plus/> <cn> 1 </cn> <cn> 2 </cn> <cn> 3 </cn> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "1 + 2 + 3" == self.F ))
pass
def test_element_ci_definitionURL(self):
s = wrapMathML("<ci definitionURL=\"foobar\"> x </ci>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_NAME)
self.assert_(("x" == self.N.getName()))
self.assert_(self.N.getNumChildren() == 0)
self.assert_(self.N.getDefinitionURL().getValue(0) == "foobar")
pass
def test_element_cn_e_notation(self):
s = wrapMathML("<cn type='e-notation'> 12.3 <sep/> 5 </cn>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_REAL_E)
self.assert_(self.N.getMantissa() == 12.3)
self.assert_(self.N.getExponent() == 5)
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_cn_rational(self):
s = wrapMathML("<cn type='rational'> 12342 <sep/> 2342342 </cn>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_RATIONAL)
self.assert_(self.N.getNumerator() == 12342)
self.assert_(self.N.getDenominator() == 2342342)
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_root_1(self):
s = wrapMathML("<apply> <root/> <degree> <cn type='integer'> 3 </cn> </degree>" +
" <ci> a </ci>" +
"</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "root(3, a)" == self.F ))
pass
def test_element_cn_units(self):
s = wrapMathMLUnits("<cn sbml:units=\"mole\"> 12345.7 </cn>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_REAL)
self.assert_(self.N.getReal() == 12345.7)
self.assert_(self.N.getUnits() == "mole")
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_log_1(self):
s = wrapMathML(
"<apply> <log/> <logbase> <cn type='integer'> 3 </cn> </logbase>" +
" <ci> x </ci>" + "</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("log(3, x)" == self.F))
pass
def test_element_root_1(self):
s = wrapMathML(
"<apply> <root/> <degree> <cn type='integer'> 3 </cn> </degree>" +
" <ci> a </ci>" + "</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("root(3, a)" == self.F))
pass
def test_element_lt(self):
s = wrapMathML(
"<apply> <lt/> <apply> <minus/> <infinity/> <infinity/> </apply>" +
" <cn>1</cn>" + "</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("lt(INF - INF, 1)" == self.F))
pass
def test_element_lt(self):
s = wrapMathML("<apply> <lt/> <apply> <minus/> <infinity/> <infinity/> </apply>" +
" <cn>1</cn>" +
"</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "lt(INF - INF, 1)" == self.F ))
pass
def test_element_log_1(self):
s = wrapMathML("<apply> <log/> <logbase> <cn type='integer'> 3 </cn> </logbase>" +
" <ci> x </ci>" +
"</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "log(3, x)" == self.F ))
pass
def test_element_bug_cn_e_notation_3(self):
s = wrapMathML("<cn type='e-notation'> -6 <sep/> -1 </cn>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.assert_(self.N.getType() == libsbml.AST_REAL_E)
self.assert_(self.N.getMantissa() == -6.0)
self.assert_(self.N.getExponent() == -1.0)
self.assert_(self.N.getNumChildren() == 0)
pass
def test_element_function_call_2(self):
s = wrapMathML("<apply> <plus/> <cn> 1 </cn>" +
" <apply> <ci> f </ci> <ci> x </ci> </apply>" +
"</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "1 + f(x)" == self.F ))
pass
