def test_from_json__customized_json_changed(self):
""" Test Reaction.from_json with a customized reaction and modified json. Ensure propensities don't change. """
test_json = {
'name': 'test_reaction',
'reactants': [{
'key': 'B',
'value': 1
}],
'products': [{
'key': 'A',
'value': 1
}],
'marate': None,
'annotation': None,
'propensity_function': '(k1*A)',
'ode_propensity_function': '(k1*A)',
'massaction': False,
'type': 'customized'
}
reaction = Reaction.from_json(test_json)
self.assertEqual(reaction.name, 'test_reaction')
self.assertEqual(reaction.reactants, {'B': 1})
self.assertEqual(reaction.products, {'A': 1})
self.assertEqual(reaction.propensity_function, '(k1*A)')
self.assertEqual(reaction.ode_propensity_function, '(k1*A)')
self.assertIsNone(reaction.marate)
self.assertIsNone(reaction.annotation)
self.assertFalse(reaction.massaction)
self.assertEqual(reaction.type, 'customized')
def test_from_json__massaction_json_changed(self):
""" Test Reaction.from_json with a mass-action reaction and modified json. Ensure propensities are updated."""
test_json = {
'name': 'test_reaction',
'reactants': [{
'key': 'B',
'value': 1
}],
'products': [{
'key': 'A',
'value': 1
}],
'marate': 'k1',
'annotation': None,
'propensity_function': '(k1*A)',
'ode_propensity_function': '(k1*A)',
'massaction': True,
'type': 'mass-action'
}
reaction = Reaction.from_json(test_json)
self.assertEqual(reaction.name, 'test_reaction')
self.assertEqual(reaction.reactants, {'B': 1})
self.assertEqual(reaction.products, {'A': 1})
self.assertEqual(reaction.propensity_function, '(k1*B)')
self.assertEqual(reaction.ode_propensity_function, '(k1*B)')
self.assertEqual(reaction.marate, 'k1')
self.assertIsNone(reaction.annotation)
self.assertTrue(reaction.massaction)
self.assertEqual(reaction.type, 'mass-action')
def test_from_json__invalid_json(self):
""" Test Reaction.from_json with a reaction that fails validation. """
test_json = {
'name': 'test_reaction',
'reactants': [{
'key': 'A',
'value': 1
}],
'products': [{
'key': 'B',
'value': 1
}],
'marate': None,
'annotation': None,
'propensity_function': '(k1*A)',
'ode_propensity_function': '(k1*A)',
'massaction': True,
'type': 'mass-action'
}
with self.assertRaises(ReactionError):
reaction = Reaction.from_json(test_json)