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_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_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 generate(self):
def mathc2p(s):
r = StringIO()
t = etree.parse(StringIO(s))
t.xslt(mathmlc2p_xslt).write(r)
return r.getvalue()
reader = libsbml.SBMLReader()
doc = reader.readSBMLFromString(self.input)
model = doc.getModel()
reactions = model.getListOfReactions()
result = []
for i in reactions:
name = i.getName()
reactants = [model.getSpecies(j.getSpecies()).getName()
for j in i.getListOfReactants()]
reversible = i.getReversible()
products = [model.getSpecies(j.getSpecies()).getName()
for j in i.getListOfProducts()]
modifiers = [model.getSpecies(j.getSpecies()).getName()
for j in i.getListOfModifiers()]
rawmath = libsbml.writeMathMLToString(i.getKineticLaw().getMath())
math = mathc2p(rawmath)
part = (name, reactants, reversible, products, modifiers, math)
result.append(part)
return (
('reactions', result),
)
def test_MathMLFormatter_cn_rational(self):
expected = wrapMathML(" <cn type=\"rational\"> 1 <sep/> 3 </cn>\n")
self.N = libsbml.ASTNode()
self.N.setValue(1, 3)
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
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_constant_infinity(self):
expected = wrapMathML(" <infinity/>\n")
self.N = libsbml.ASTNode()
self.N.setValue(util_PosInf())
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_constant_notanumber(self):
expected = wrapMathML(" <notanumber/>\n")
self.N = libsbml.ASTNode(libsbml.AST_REAL)
self.N.setValue(util_NaN())
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_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 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_constant_notanumber(self):
expected = wrapMathML(" <notanumber/>\n")
self.N = libsbml.ASTNode(libsbml.AST_REAL)
self.N.setValue( util_NaN() )
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_MathMLFormatter_csymbol_time(self):
expected = wrapMathML(" <csymbol encoding=\"text\" " + "definitionURL=\"http://www.sbml.org/sbml/symbols/time\"> t </csymbol>\n")
self.N = libsbml.ASTNode(libsbml.AST_NAME_TIME)
self.N.setName("t")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def astnode_to_mathml(astnode: libsbml.ASTNode) -> str:
"""Convert to MathML string representation.
:param astnode: ASTNode instance
:return string rendering of MathML content for the ASTNode instance
"""
return libsbml.writeMathMLToString(astnode) # type: ignore
def test_MathMLFormatter_constant_infinity(self):
expected = wrapMathML(" <infinity/>\n")
self.N = libsbml.ASTNode()
self.N.setValue( util_PosInf() )
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
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_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_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 test_MathMLFormatter_cn_rational(self):
expected = wrapMathML(" <cn type=\"rational\"> 1 <sep/> 3 </cn>\n"
)
self.N = libsbml.ASTNode()
self.N.setValue(1,3)
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
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 formula_to_mathml(string: str) -> str:
"""Parse formula string.
:param string: formula string
:return string rendering of parsed formula in the formula string
"""
astnode = libsbml.parseL3Formula(str(string))
mathml = libsbml.writeMathMLToString(astnode)
return str(mathml)
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_MathMLFormatter_plus_binary(self):
expected = wrapMathML(" <apply>\n" + " <plus/>\n" +
" <cn type=\"integer\"> 1 </cn>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </apply>\n")
self.N = libsbml.parseFormula("1 + 2")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_plus_binary(self):
expected = wrapMathML(" <apply>\n" +
" <plus/>\n" +
" <cn type=\"integer\"> 1 </cn>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </apply>\n")
self.N = libsbml.parseFormula("1 + 2")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_csymbol_time(self):
expected = wrapMathML(
" <csymbol encoding=\"text\" " +
"definitionURL=\"http://www.sbml.org/sbml/symbols/time\"> t </csymbol>\n"
)
self.N = libsbml.ASTNode(libsbml.AST_NAME_TIME)
self.N.setName("t")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_lambda_no_bvars(self):
expected = wrapMathML(" <lambda>\n" + " <apply>\n" +
" <plus/>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </apply>\n" + " </lambda>\n")
self.N = libsbml.parseFormula("lambda(2 + 2)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_function_1(self):
expected = wrapMathML(" <apply>\n" + " <ci> foo </ci>\n" +
" <cn type=\"integer\"> 1 </cn>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" <cn type=\"integer\"> 3 </cn>\n" +
" </apply>\n")
self.N = libsbml.parseFormula("foo(1, 2, 3)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_log(self):
expected = wrapMathML(" <apply>\n" + " <log/>\n" +
" <logbase>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </logbase>\n" + " <ci> N </ci>\n" +
" </apply>\n")
self.N = libsbml.parseFormula("log(2, N)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_root(self):
expected = wrapMathML(" <apply>\n" + " <root/>\n" +
" <degree>\n" +
" <cn type=\"integer\"> 3 </cn>\n" +
" </degree>\n" + " <ci> x </ci>\n" +
" </apply>\n")
self.N = libsbml.parseFormula("root(3, x)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_function_1(self):
expected = wrapMathML(" <apply>\n" +
" <ci> foo </ci>\n" +
" <cn type=\"integer\"> 1 </cn>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" <cn type=\"integer\"> 3 </cn>\n" +
" </apply>\n")
self.N = libsbml.parseFormula("foo(1, 2, 3)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_csymbol_delay(self):
expected = wrapMathML(
" <apply>\n" +
" <csymbol encoding=\"text\" definitionURL=\"http://www.sbml.org/sbml/"
+ "symbols/delay\"> my_delay </csymbol>\n" + " <ci> x </ci>\n" +
" <cn> 0.1 </cn>\n" + " </apply>\n")
self.N = libsbml.parseFormula("delay(x, 0.1)")
self.N.setName("my_delay")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_csymbol_delay(self):
expected = wrapMathML(" <apply>\n" +
" <csymbol encoding=\"text\" definitionURL=\"http://www.sbml.org/sbml/" +
"symbols/delay\"> my_delay </csymbol>\n" +
" <ci> x </ci>\n" +
" <cn> 0.1 </cn>\n" +
" </apply>\n")
self.N = libsbml.parseFormula("delay(x, 0.1)")
self.N.setName("my_delay")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_root(self):
expected = wrapMathML(" <apply>\n" +
" <root/>\n" +
" <degree>\n" +
" <cn type=\"integer\"> 3 </cn>\n" +
" </degree>\n" +
" <ci> x </ci>\n" +
" </apply>\n")
self.N = libsbml.parseFormula("root(3, x)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def _get_math(formula, parameters):
'''Returns math element from formula and parameters.'''
math_elem = '<math xmlns="http://www.w3.org/1998/Math/MathML">'
param_str = math_elem + '<lambda>'
for parameter in parameters:
param_str += '<bvar><ci>' + parameter + '</ci></bvar>'
mathml = libsbml.writeMathMLToString(libsbml.parseFormula(formula))
mathml = mathml.replace(math_elem, param_str)
mathml = mathml.replace('</math>', '</lambda></math>')
return libsbml.readMathMLFromString(mathml)
def test_MathMLFormatter_log(self):
expected = wrapMathML(" <apply>\n" +
" <log/>\n" +
" <logbase>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </logbase>\n" +
" <ci> N </ci>\n" +
" </apply>\n")
self.N = libsbml.parseFormula("log(2, N)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_lambda_no_bvars(self):
expected = wrapMathML(" <lambda>\n" +
" <apply>\n" +
" <plus/>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" <cn type=\"integer\"> 2 </cn>\n" +
" </apply>\n" +
" </lambda>\n")
self.N = libsbml.parseFormula("lambda(2 + 2)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_piecewise_otherwise(self):
expected = wrapMathML(" <piecewise>\n" + " <piece>\n" +
" <cn type=\"integer\"> 0 </cn>\n" +
" <apply>\n" + " <lt/>\n" +
" <ci> x </ci>\n" +
" <cn type=\"integer\"> 0 </cn>\n" +
" </apply>\n" + " </piece>\n" +
" <otherwise>\n" + " <ci> x </ci>\n" +
" </otherwise>\n" + " </piecewise>\n")
self.N = libsbml.parseFormula("piecewise(0, lt(x, 0), x)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_piecewise_otherwise(self):
expected = wrapMathML(" <piecewise>\n" +
" <piece>\n" +
" <cn type=\"integer\"> 0 </cn>\n" +
" <apply>\n" +
" <lt/>\n" +
" <ci> x </ci>\n" +
" <cn type=\"integer\"> 0 </cn>\n" +
" </apply>\n" +
" </piece>\n" +
" <otherwise>\n" +
" <ci> x </ci>\n" +
" </otherwise>\n" +
" </piecewise>\n")
self.N = libsbml.parseFormula("piecewise(0, lt(x, 0), x)")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
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 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 astnode_to_mathml(astnode: libsbml.ASTNode) -> str:
"""Convert to MathML string representation."""
return libsbml.writeMathMLToString(astnode)
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 astnodeToMathML(astnode):
mathml = libsbml.writeMathMLToString(astnode)
return mathml
def test_MathMLFormatter_constant_true(self):
expected = wrapMathML(" <true/>\n")
self.N = libsbml.ASTNode(libsbml.AST_CONSTANT_TRUE)
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_cn_real_2(self):
expected = wrapMathML(" <cn> 1234567.8 </cn>\n")
self.N = libsbml.parseFormula("1234567.8")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def test_MathMLFormatter_cn_real_locale(self):
expected = wrapMathML(" <cn> 2.72 </cn>\n")
self.N = libsbml.parseFormula("2.72")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_cn_real_2(self):
expected = wrapMathML(" <cn> 1234567.8 </cn>\n")
self.N = libsbml.parseFormula("1234567.8")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
def test_MathMLFormatter_constant_true(self):
expected = wrapMathML(" <true/>\n")
self.N = libsbml.ASTNode(libsbml.AST_CONSTANT_TRUE)
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def stringToMathML(string):
"""Parses formula string. """
astnode = libsbml.parseL3Formula(str(string))
mathml = libsbml.writeMathMLToString(astnode)
return mathml
def astnode_to_latex(astnode: libsbml.ASTNode) -> str:
"""Convert ASTNode to Latex using XSLT transformation."""
cmml_str: str = libsbml.writeMathMLToString(astnode)
cmml_str = cmml_str.replace('<?xml version="1.0" encoding="UTF-8"?>', "")
return cmathml_to_latex(cmml_str)
def test_MathMLFormatter_cn_real_locale(self):
expected = wrapMathML(" <cn> 2.72 </cn>\n")
self.N = libsbml.parseFormula("2.72")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def formula_to_mathml(string: str) -> str:
"""Parses formula string. """
astnode = libsbml.parseL3Formula(str(string))
mathml = libsbml.writeMathMLToString(astnode)
return mathml
def test_MathMLFormatter_ci(self):
expected = wrapMathML(" <ci> foo </ci>\n")
self.N = libsbml.parseFormula("foo")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual(True, self.equals(expected, self.S))
pass
def astnodeToMathML(astnode):
mathml = libsbml.writeMathMLToString(astnode)
return mathml
def test_MathMLFormatter_ci(self):
expected = wrapMathML(" <ci> foo </ci>\n")
self.N = libsbml.parseFormula("foo")
self.S = libsbml.writeMathMLToString(self.N)
self.assertEqual( True, self.equals(expected,self.S) )
pass
