def test_read_task(self):
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('ignored before content\n')
file.write('\n')
file.write('begin model\n')
file.write('begin parameters\n')
file.write(' k_1 0.0\n')
file.write(' # k_2 0.0\n')
file.write('end parameters\n')
file.write('end model\n')
file.write('\n')
file.write('ode\n')
with pytest.warns(IgnoredBnglFileContentWarning,
match='outside content blocks were ignored'):
task = read_task(filename)
self.assertTrue(
task.model.is_equal(Model({'parameters':
ModelBlock(['k_1 0.0'])})))
task.actions = ['ode']
read_task(
os.path.join(os.path.dirname(__file__), 'fixtures', 'test.bngl'))
read_task(
os.path.join(os.path.dirname(__file__), 'fixtures', 'dolan.bngl'))
def test_get_parameters_variables_outputs_for_simulation(self):
fixtures_dirname = os.path.join(os.path.dirname(__file__), 'fixtures')
for model_filename in [
os.path.join(fixtures_dirname, 'test.bngl'),
os.path.join(fixtures_dirname, 'LR_comp_resolved.bngl'),
]:
changes, sim, variables, plots = get_parameters_variables_outputs_for_simulation(
model_filename, None, UniformTimeCourseSimulation, None)
task = read_task(model_filename)
task.actions = []
for change in changes:
add_model_attribute_change_to_task(task, change)
add_variables_to_model(task.model, variables)
model_filename_2 = os.path.join(self.dirname, 'task.bngl')
write_task(task, model_filename_2)
changes_2, sim, variables_2, plots_2 = get_parameters_variables_outputs_for_simulation(
model_filename_2, None, UniformTimeCourseSimulation, None)
for change, change_2 in zip(changes, changes_2):
self.assertTrue(change_2.is_equal(change))
for variable, variable_2 in zip(variables, variables_2):
self.assertTrue(variable_2.is_equal(variable))
task_2 = read_task(model_filename_2)
self.assertEqual(task_2.model, task.model)
def test_add_model_attribute_change_to_task(self):
model_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'test.bngl')
task = read_task(model_filename)
task.model['compartments'] = [
'EC 3 vol_EC',
'PM 2 sa_PM*eff_width EC',
]
change = ModelAttributeChange(target='compartments.EC.size', new_value='0.5')
add_model_attribute_change_to_task(task, change)
self.assertEqual(task.model['compartments'], [
'EC 3 0.5',
'PM 2 sa_PM*eff_width EC',
])
task = read_task(model_filename)
change = ModelAttributeChange(target='functions.gfunc().expression', new_value='0.5')
add_model_attribute_change_to_task(task, change)
self.assertEqual(task.model['functions'], ['gfunc() = 0.5'])
task = read_task(model_filename)
change = ModelAttributeChange(target='functions.gfunc.expression', new_value='0.5')
add_model_attribute_change_to_task(task, change)
self.assertEqual(task.model['functions'], ['gfunc() = 0.5'])
change = ModelAttributeChange(target='parameters.k_1.value', new_value='1.0')
add_model_attribute_change_to_task(task, change)
self.assertEqual(task.actions[-1], 'setParameter("k_1", 1.0)')
change = ModelAttributeChange(target='species.GeneA_00().initialCount', new_value='1')
add_model_attribute_change_to_task(task, change)
self.assertEqual(task.actions[-1], 'setConcentration("GeneA_00()", 1)')
# error: no compartment
task = read_task(model_filename)
task.model['compartments'] = [
'EC 3 vol_EC',
'PM 2 sa_PM*eff_width EC',
]
change = ModelAttributeChange(target='compartments.CE.size', new_value='0.5')
with self.assertRaisesRegex(ValueError, 'the model does not have a compartment'):
add_model_attribute_change_to_task(task, change)
# error: no function
change = ModelAttributeChange(target='functions.hfunc.expression', new_value='0.5')
with self.assertRaisesRegex(ValueError, 'the model does not have a function'):
add_model_attribute_change_to_task(task, change)
# error: no function
change = ModelAttributeChange(target='functions.hfunc().expression', new_value='0.5')
with self.assertRaisesRegex(ValueError, 'the model does not have a function'):
add_model_attribute_change_to_task(task, change)
# error: no function
change = ModelAttributeChange(target='section.object.attribute', new_value='0.5')
with self.assertRaisesRegex(NotImplementedError, 'is not a valid target'):
add_model_attribute_change_to_task(task, change)
def test_exec_bionetgen_task(self):
model_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'test.bngl')
task = read_task(model_filename)
results = exec_bionetgen_task(task)
self.assertEqual(set(results.index), set([
'time',
'Atot',
'Btot',
'GA00tot',
'GA01tot',
'GA10tot',
'GB00tot',
'GB01tot',
'GB10tot',
]))
self.assertFalse(numpy.any(numpy.isnan(results)))
numpy.testing.assert_allclose(results.loc['time', :], numpy.linspace(0., 1000000., 1000 + 1))
# error handling
with mock.patch('subprocess.check_call', side_effect=ValueError('big error')):
with self.assertRaisesRegex(ValueError, 'big error'):
exec_bionetgen_task(task)
def test_add_variables_to_task(self):
model_filename = os.path.join(os.path.dirname(__file__), 'fixtures',
'test.bngl')
task = read_task(model_filename)
task.model.pop('observables')
variables = [
Variable(id='Time', symbol=Symbol.time),
Variable(id='A', target='species.A'),
Variable(id='B', target='species.B.count'),
Variable(id='Atot', target='molecules.A()'),
Variable(id='GA00tot', target='molecules.GeneA_00().count'),
]
add_variables_to_model(task.model, variables)
self.assertEqual(task.model['observables'], [
'Species A A',
'Species B B',
'Molecules Atot A()',
'Molecules GA00tot GeneA_00()',
])
task.model.move_to_end('functions')
task.model.move_to_end('reaction rules')
results = exec_bionetgen_task(task)
self.assertEqual(set(results.index),
set([
'time',
'A',
'B',
'Atot',
'GA00tot',
]))
add_variables_to_model(task.model, [])
self.assertEqual(task.model['observables'], [
'Species A A',
'Species B B',
'Molecules Atot A()',
'Molecules GA00tot GeneA_00()',
])
# error handling
with self.assertRaisesRegex(NotImplementedError,
'symbols are not supported'):
add_variables_to_model(task.model, [Variable(id='X', symbol='x')])
with self.assertRaisesRegex(NotImplementedError,
'targets are not supported'):
add_variables_to_model(task.model, [Variable(id='X', target='x')])
def test_write_task(self):
task = Task()
model = task.model = Model()
model['parameters'] = ModelBlock([
'k_1 0.0',
'r_2 0.0',
])
model['molecule types'] = ModelBlock([
'A()',
'B()',
'C()',
])
task.actions = ['ode', 'nf']
filename = os.path.join(self.dirname, 'task.bngl')
write_task(task, filename)
with open(filename, 'r') as file:
lines = file.readlines()
self.assertEqual(lines, [
'begin model\n',
'begin parameters\n',
' k_1 0.0\n',
' r_2 0.0\n',
'end parameters\n',
'begin molecule types\n',
' A()\n',
' B()\n',
' C()\n',
'end molecule types\n',
'end model\n',
'ode\n',
'nf\n',
])
task2 = read_task(filename)
self.assertTrue(task2.is_equal(task))
def test_read_task_error_handling(self):
# no `begin model`
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('\n')
with self.assertRaisesRegex(ValueError, 'does not contain a model'):
read_task(filename)
# no `end model`
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('begin model\n')
with self.assertRaisesRegex(ValueError, 'has no termination'):
read_task(filename)
# no `begin model`
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('begin parameters\n')
with self.assertRaisesRegex(ValueError, 'has no termination'):
read_task(filename)
# two parameters blocks
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('begin model\n')
file.write('begin parameters\n')
file.write(' k_1 0.0\n')
file.write('end parameters\n')
file.write('begin parameters\n')
file.write(' k_2 0.0\n')
file.write('end parameters\n')
file.write('end model\n')
with self.assertRaisesRegex(ValueError, 'has a second'):
read_task(filename)
# no triple nesting of block
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('begin model\n')
file.write('begin parameters\n')
file.write(' begin parameters\n')
file.write(' end parameters\n')
file.write('end parameters\n')
file.write('end model\n')
with self.assertRaisesRegex(ValueError, 'is inappropriately nested'):
read_task(filename)
# mismatched ending
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('begin model\n')
file.write('begin parameters\n')
file.write('end reactions\n')
file.write('end model\n')
with self.assertRaisesRegex(ValueError, 'incorrectly ends'):
read_task(filename)
# inappropriately nested content
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('begin model\n')
file.write(' k_1 0.0\n')
file.write('end model\n')
with pytest.warns(IgnoredBnglFileContentWarning,
match='outside content blocks were ignored'):
read_task(filename)
# inappropriately nested content
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('begin parameters\n')
file.write('begin parameters\n')
file.write(' k_1 0.0\n')
file.write('end parameters\n')
file.write('end parameters\n')
with self.assertRaisesRegex(ValueError, 'inappropriately nested'):
read_task(filename)
# no second model
filename = os.path.join(self.dirname, 'model.bngl')
with open(filename, 'w') as file:
file.write('begin model\n')
file.write(' k_1 0.0\n')
file.write('end model\n')
file.write('begin model\n')
file.write(' k_1 0.0\n')
file.write('end model\n')
with self.assertRaisesRegex(ValueError, 'contains a second model'):
read_task(filename)