def test_units(self): # Test writing of units u1 = myokit.parse_unit('kg*m^2/mole^3 (0.123)') m1 = cellml.Model('mmm') m1.add_units('flibbit', u1) m1.add_units('special_volt', myokit.units.Volt) d = m1.add_component('ddd') q = d.add_variable('q', 'flibbit') q.set_equation(myokit.Equation(myokit.Name(q), myokit.Number(2, u1))) xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) q = m2['ddd']['q'] self.assertEqual(q.units().name(), 'flibbit') self.assertEqual(q.units().myokit_unit(), u1) self.assertEqual( m2.find_units('special_volt').myokit_unit(), myokit.units.volt) # Dimensionless units with a multiplier u1 = myokit.parse_unit('1 (0.123)') m1 = cellml.Model('mmm') m1.add_units('flibbit', u1) xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) u2 = m2.find_units('flibbit') u2 = u2.myokit_unit() self.assertEqual(u1, u2)
def test_encapsulation(self): # Tests if encapsulation relationships are written out. # Create a model with # d # a e # f c # b # m1 = cellml.Model('m') a = m1.add_component('a') b = m1.add_component('b') c = m1.add_component('c') d = m1.add_component('d') e = m1.add_component('e') f = m1.add_component('f') a.set_parent(d) e.set_parent(d) f.set_parent(e) c.set_parent(e) b.set_parent(c) xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) a, b, c, d, e, f = [m2.component(x) for x in 'abcdef'] self.assertIs(a.parent(), d) self.assertIs(e.parent(), d) self.assertIs(f.parent(), e) self.assertIs(c.parent(), e) self.assertIs(b.parent(), c)
def test_connections(self): # Tests if connections are written m1 = cellml.Model('m') c = m1.add_component('c') d = m1.add_component('d') p = c.add_variable('p', 'mole', 'public') q = d.add_variable('q', 'mole', 'public') r = c.add_variable('r', 'ampere', 'public') s = d.add_variable('r', 'ampere', 'public') p.set_initial_value(1) s.set_initial_value(2) m1.add_connection(p, q) m1.add_connection(r, s) xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) p = m2['c']['p'] q = m2['d']['q'] self.assertIn(p, q.connected_variables()) self.assertIn(q, p.connected_variables()) self.assertIs(p.initial_value_variable(), p) self.assertIs(q.initial_value_variable(), p) r = m2['c']['r'] s = m2['d']['r'] self.assertIn(r, s.connected_variables()) self.assertIn(s, r.connected_variables()) self.assertIs(r.initial_value_variable(), s) self.assertIs(s.initial_value_variable(), s)
def test_variable(self): # Tests writing of variables m1 = cellml.Model('m') c = m1.add_component('c') p = c.add_variable('p', 'mole') q = c.add_variable('q', 'kelvin', interface='public') r = c.add_variable('r', 'ampere', interface='private') p.set_initial_value(1) with WarningCollector(): xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) p, q, r = m2['c']['p'], m2['c']['q'], m2['c']['r'] self.assertEqual(p.units().name(), 'mole') self.assertEqual(q.units().name(), 'kelvin') self.assertEqual(r.units().name(), 'ampere') self.assertEqual(p.interface(), 'none') self.assertEqual(q.interface(), 'public') self.assertEqual(r.interface(), 'private') self.assertEqual(p.initial_value(), myokit.Number(1, myokit.units.mole)) self.assertEqual(q.initial_value(), None) self.assertEqual(r.initial_value(), None)
def test_version(self): # Tests if all supported versions can be written # Version 2.0 m1 = cellml.Model('m', version='2.0') xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) self.assertEqual(m2.version(), '2.0')
def test_write_string(self): # Tests write_string m1 = cellml.Model('ernie') xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) self.assertEqual(m2.name(), 'ernie') self.assertEqual(len(m2), 0)
def test_model(self): # Tests model writing m1 = cellml.Model('model_name') xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) self.assertEqual(m2.name(), 'model_name') self.assertEqual(len(m2), 0)
def test_component(self): # Tests if components are written m1 = cellml.Model('m') c = m1.add_component('c') d = m1.add_component('d') xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) self.assertIn('c', m2) self.assertIn('d', m2)
def _test_maths(self, version): # Test maths is written (in selected ``version``) # Create model m1 = cellml.Model('m', version) c1 = m1.add_component('c') p1 = c1.add_variable('p', 'mole') p1.set_initial_value(2) q1 = c1.add_variable('q', 'dimensionless') r1 = c1.add_variable('r', 'second') r1.set_initial_value(0.1) t1 = c1.add_variable('t', 'second') m1.set_variable_of_integration(t1) # Add component without maths d1 = m1.add_component('d') s1 = d1.add_variable('s', 'volt') s1.set_initial_value(1.23) # Add two equations # Note: Numbers without units become dimensionless in CellML eq1 = myokit.Equation( myokit.Name(q1), myokit.Plus(myokit.Number(3, myokit.units.mole), myokit.Name(p1))) er1 = myokit.Equation(myokit.Derivative(myokit.Name(r1)), myokit.Power(myokit.Name(q1), myokit.Number(2))) q1.set_equation(eq1) r1.set_equation(er1) # Write and read xml = cellml.write_string(m1) m2 = cellml.parse_string(xml) # Check results p2, q2, r2, s2 = m2['c']['p'], m2['c']['q'], m2['c']['r'], m2['d']['s'] subst = { myokit.Name(p1): myokit.Name(p2), myokit.Name(q1): myokit.Name(q2), myokit.Name(r1): myokit.Name(r2), } eq2 = eq1.clone(subst) er2 = er1.clone(subst) self.assertEqual(q2.equation(), eq2) self.assertEqual(r2.equation(), er2) self.assertEqual(s2.initial_value(), myokit.Number(1.23, myokit.units.volt)) self.assertFalse(p2.is_state()) self.assertFalse(q2.is_state()) self.assertTrue(r2.is_state()) self.assertFalse(s2.is_state()) self.assertIs(m2.variable_of_integration(), m2['c']['t'])
def test_evaluating_derivatives(self): # Writes and then parses a model and compares the derivatives m1 = myokit.load_model('example') c1 = cellml.Model.from_myokit_model(m1) xml = cellml.write_string(c1) c2 = cellml.parse_string(xml) m2 = c2.myokit_model() self.assertEqual( m1.get('membrane.V').eval(), m2.get('membrane.V').eval()) self.assertEqual(m1.get('ina.m').eval(), m2.get('ina.m').eval()) self.assertEqual(m1.get('ina.h').eval(), m2.get('ina.h').eval()) self.assertEqual(m1.get('ina.j').eval(), m2.get('ina.j').eval()) self.assertEqual(m1.get('ica.d').eval(), m2.get('ica.d').eval()) self.assertEqual(m1.get('ica.f').eval(), m2.get('ica.f').eval()) self.assertEqual(m1.get('ik.x').eval(), m2.get('ik.x').eval()) self.assertEqual(m1.get('ica.Ca_i').eval(), m2.get('ica.Ca_i').eval())
def parse(self, xml, version='2.0'): """ Inserts the given ``xml`` into a <model> element, parses it, and returns the result. """ return v2.parse_string(self.wrap(xml, version))
def test_model(self): # Tests parsing a model element. # Valid one is already tested # Invalid namespace x = '<?xml version="1.0" encoding="UTF-8"?>' y = '<model name="x" xmlns="http://example.com" />' self.assertRaisesRegex(v2.CellMLParsingError, 'must be in CellML', v2.parse_string, x + y) # CellML 2.0 is ok y = '<model name="x" xmlns="http://www.cellml.org/cellml/2.0#" />' m = v2.parse_string(x + y) self.assertEqual(m.version(), '2.0') # Not a model y = '<module name="x" xmlns="http://www.cellml.org/cellml/2.0#" />' self.assertRaisesRegex(v2.CellMLParsingError, 'must be a CellML model', v2.parse_string, x + y) # No name y = '<model xmlns="http://www.cellml.org/cellml/2.0#" />' self.assertRaisesRegex(v2.CellMLParsingError, 'Model element must have a name', v2.parse_string, x + y) # CellML API errors are wrapped y = '<model name="123" xmlns="http://www.cellml.org/cellml/2.0#" />' self.assertRaisesRegex(v2.CellMLParsingError, 'valid CellML identifier', v2.parse_string, x + y) # Too many free variables self.assertBad( '<component name="a">' ' <variable name="x" units="dimensionless" initial_value="0.1" />' ' <variable name="y" units="dimensionless" initial_value="2.3" />' ' <variable name="time1" units="dimensionless" />' ' <variable name="time2" units="dimensionless" />' ' <math xmlns="http://www.w3.org/1998/Math/MathML">' ' <apply>' ' <eq />' ' <apply>' ' <diff/>' ' <bvar>' ' <ci>time1</ci>' ' </bvar>' ' <ci>x</ci>' ' </apply>' ' <cn cellml:units="dimensionless">1</cn>' ' </apply>' ' <apply>' ' <eq />' ' <apply>' ' <diff/>' ' <bvar>' ' <ci>time2</ci>' ' </bvar>' ' <ci>y</ci>' ' </apply>' ' <cn cellml:units="dimensionless">2</cn>' ' </apply>' ' </math>' '</component>', 'derivatives with respect to more than one variable')