def add_sims_from_exp_to_study(study,
experiment_names,
first_simulated_step_name,
last_simulated_step_name,
initial_buffer_name=None):
""" Create simulations from experiments and add them to study.
Parameters
----------
study : Study
Study to which to add new simulations.
experiment_names : list(str)
List of experiment names to create the simulations from.
first_simulated_step_name : str
Name of the method step to start the simulation's method.
last_simulated_step_name : str
Name of the method step to end the simulation's method.
initial_buffer_name : str [OPTIONAL]
Name of the buffer to use for initial condition. If not set, it will be
derived from first_simulated_step_name.
"""
from kromatography.ui.simulation_from_experiment_builder import \
SimulationFromExperimentBuilder
sim_builder = SimulationFromExperimentBuilder(
target_study=study,
first_simulated_step_name=first_simulated_step_name,
last_simulated_step_name=last_simulated_step_name,
initial_buffer_name=initial_buffer_name)
sim_builder.experiment_selector.experiment_selected = experiment_names
study.simulations.extend(sim_builder.to_simulations())
def test_build_1sim(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip")
sim_builder.experiment_selector.experiment_selected = ['Run_1']
sims = sim_builder.to_simulations()
self.assertEqual(len(sims), 1)
self.assertValidSimulations(sims, self.study2)
def test_init_buffers_come_from_explicit_value(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip",
initial_buffer_name="Strip_1")
exps = ['Run_1', 'Run_2']
sim_builder.experiment_selector.experiment_selected = exps
sims = sim_builder.to_simulations()
for sim in sims:
self.assertEqual(sim.method.initial_buffer.name, "Strip_1")
def test_build_1sim_no_method_bounds(self):
sim_builder = SimulationFromExperimentBuilder(target_study=self.study2)
sim_builder.experiment_selector.experiment_selected = ['Run_1']
sims = sim_builder.to_simulations()
self.assertEqual(len(sims), 1)
# first and last step names are the default value in the sim_builder
# since nothing was passed.
flstep = sim_builder.first_simulated_step_name
# Don't check the product because there is no load in this sim...
self.assertValidSimulations(sims,
self.study2,
fstep=flstep,
lstep=flstep,
check_product=False)
def request_new_simulations_from_experiments(self):
""" Add new simulations mirroring experiment(s) in the current study.
"""
from kromatography.ui.simulation_from_experiment_builder import \
SimulationFromExperimentBuilder
from kromatography.ui.experiment_selector import ExperimentSelector
sim_builder = SimulationFromExperimentBuilder(
experiment_selector=ExperimentSelector(study=self),
target_study=self,
)
ui = sim_builder.edit_traits(kind="livemodal")
if ui.result:
new_sims = sim_builder.to_simulations()
self.simulations.extend(new_sims)
def test_cannot_create(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip",
initial_buffer_name="Strip_1")
self.assertFalse(sim_builder.can_create)
with self.assertTraitChanges(sim_builder, "can_create"):
sim_builder.experiment_selector.experiment_selected = ['Run_1']
self.assertTrue(sim_builder.can_create)
def test_different_init_buffers_from_different_exp_method(self):
# Set each exp to a different initial condition:
initial_condition_step = 1
exp_names = ['Run_1', 'Run_2']
experiments = [
self.study2.search_experiment_by_name(name) for name in exp_names
]
for exp in experiments:
buf = Buffer(name="New buf for {}".format(exp.name))
exp.method.method_steps[initial_condition_step].solutions = [buf]
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip")
sim_builder.experiment_selector.experiment_selected = exp_names
sims = sim_builder.to_simulations()
for sim, exp_name in zip(sims, exp_names):
buf_name = "New buf for {}".format(exp_name)
self.assertEqual(sim.method.initial_buffer.name, buf_name)
def test_build_1sim_from_method_start(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name='Pre-Equilibration',
last_simulated_step_name="Strip")
sim_builder.experiment_selector.experiment_selected = ['Run_1']
# Fail because no initial_buffer specified, and no step before:
with self.assertRaises(ValueError):
sim_builder.to_simulations()
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name='Pre-Equilibration',
last_simulated_step_name="Strip",
initial_buffer_name="Equil_Wash_1")
sim_builder.experiment_selector.experiment_selected = ['Run_1']
sims = sim_builder.to_simulations()
self.assertEqual(len(sims), 1)
# Init buffer read from experimental method:
self.assertEqual(sims[0].method.initial_buffer.name, 'Equil_Wash_1')
self.assertValidSimulations(sims,
self.study2,
fstep='Pre-Equilibration')
def test_create_builder(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip")
self.assertIsInstance(sim_builder, SimulationFromExperimentBuilder)
def test_create_builder_no_method_bounds(self):
sim_builder = SimulationFromExperimentBuilder(target_study=self.study2)
self.assertIsInstance(sim_builder, SimulationFromExperimentBuilder)
def test_create_builder_no_arg(self):
with self.assertRaises(ValueError):
SimulationFromExperimentBuilder()
def setUp(self):
self.study = make_sample_study(num_exp=5)
self.sim_builder = SimulationFromExperimentBuilder(
experiment_selector=ExperimentSelector(study=self.study),
target_study=self.study,
)
class TestSimulationFromExperimentBuilder(TestCase, UnittestTools):
@classmethod
def setUpClass(cls):
cls.study2 = make_sample_study2(add_transp_bind_models=True)
def setUp(self):
self.study = make_sample_study(num_exp=5)
self.sim_builder = SimulationFromExperimentBuilder(
experiment_selector=ExperimentSelector(study=self.study),
target_study=self.study,
)
def test_bring_up(self):
ui = self.sim_builder.edit_traits()
ui.dispose()
def test_create_builder_no_arg(self):
with self.assertRaises(ValueError):
SimulationFromExperimentBuilder()
def test_create_builder_no_method_bounds(self):
sim_builder = SimulationFromExperimentBuilder(target_study=self.study2)
self.assertIsInstance(sim_builder, SimulationFromExperimentBuilder)
def test_create_builder(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip")
self.assertIsInstance(sim_builder, SimulationFromExperimentBuilder)
def test_build_sim_names(self):
select = self.study.experiments[:2]
self.sim_builder.experiment_selector.experiment_selected = \
[expt.name for expt in select]
expected = [generate_sim_name(expt.name) for expt in select]
self.assertEqual(self.sim_builder.simulation_names, expected)
def test_rotate_names(self):
# Make some fake simulations to force new simulations to be appended a
# suffix:
first_exp_name = self.study.experiments[0].name
sim = Simulation(name=generate_sim_name(first_exp_name))
fake_rotated_sim_name = generate_sim_name(first_exp_name) + "_v2"
sim2 = Simulation(name=fake_rotated_sim_name)
self.study.simulations.extend([sim, sim2])
select = self.study.experiments[:2]
self.sim_builder.experiment_selector.experiment_selected = \
[expt.name for expt in select]
expected = [generate_sim_name(expt.name) for expt in select]
expected[0] += "_v3"
self.assertEqual(self.sim_builder.simulation_names, expected)
def test_build_1sim(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip")
sim_builder.experiment_selector.experiment_selected = ['Run_1']
sims = sim_builder.to_simulations()
self.assertEqual(len(sims), 1)
self.assertValidSimulations(sims, self.study2)
def test_build_1sim_no_method_bounds(self):
sim_builder = SimulationFromExperimentBuilder(target_study=self.study2)
sim_builder.experiment_selector.experiment_selected = ['Run_1']
sims = sim_builder.to_simulations()
self.assertEqual(len(sims), 1)
# first and last step names are the default value in the sim_builder
# since nothing was passed.
flstep = sim_builder.first_simulated_step_name
# Don't check the product because there is no load in this sim...
self.assertValidSimulations(sims,
self.study2,
fstep=flstep,
lstep=flstep,
check_product=False)
def test_build_2sims(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip")
sim_builder.experiment_selector.experiment_selected = [
'Run_1', 'Run_2'
]
sims = sim_builder.to_simulations()
self.assertEqual(len(sims), 2)
self.assertValidSimulations(sims, self.study2)
def test_build_1sim_from_method_start(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name='Pre-Equilibration',
last_simulated_step_name="Strip")
sim_builder.experiment_selector.experiment_selected = ['Run_1']
# Fail because no initial_buffer specified, and no step before:
with self.assertRaises(ValueError):
sim_builder.to_simulations()
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name='Pre-Equilibration',
last_simulated_step_name="Strip",
initial_buffer_name="Equil_Wash_1")
sim_builder.experiment_selector.experiment_selected = ['Run_1']
sims = sim_builder.to_simulations()
self.assertEqual(len(sims), 1)
# Init buffer read from experimental method:
self.assertEqual(sims[0].method.initial_buffer.name, 'Equil_Wash_1')
self.assertValidSimulations(sims,
self.study2,
fstep='Pre-Equilibration')
def test_different_init_buffers_from_different_exp_method(self):
# Set each exp to a different initial condition:
initial_condition_step = 1
exp_names = ['Run_1', 'Run_2']
experiments = [
self.study2.search_experiment_by_name(name) for name in exp_names
]
for exp in experiments:
buf = Buffer(name="New buf for {}".format(exp.name))
exp.method.method_steps[initial_condition_step].solutions = [buf]
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip")
sim_builder.experiment_selector.experiment_selected = exp_names
sims = sim_builder.to_simulations()
for sim, exp_name in zip(sims, exp_names):
buf_name = "New buf for {}".format(exp_name)
self.assertEqual(sim.method.initial_buffer.name, buf_name)
def test_init_buffers_come_from_explicit_value(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip",
initial_buffer_name="Strip_1")
exps = ['Run_1', 'Run_2']
sim_builder.experiment_selector.experiment_selected = exps
sims = sim_builder.to_simulations()
for sim in sims:
self.assertEqual(sim.method.initial_buffer.name, "Strip_1")
def test_cannot_create(self):
sim_builder = SimulationFromExperimentBuilder(
target_study=self.study2,
first_simulated_step_name="Load",
last_simulated_step_name="Strip",
initial_buffer_name="Strip_1")
self.assertFalse(sim_builder.can_create)
with self.assertTraitChanges(sim_builder, "can_create"):
sim_builder.experiment_selector.experiment_selected = ['Run_1']
self.assertTrue(sim_builder.can_create)
# Utilities ---------------------------------------------------------------
def assertValidSimulations(self,
sims,
target_study,
fstep='Load',
lstep="Strip",
check_product=True):
existing_sim_names = [sim.name for sim in target_study.simulations]
for sim in sims:
self.assertNotIn(sim.name, existing_sim_names)
self.assertIsInstance(sim.method, Method)
self.assertEqual(sim.method.method_steps[0].name, fstep)
self.assertEqual(sim.method.method_steps[-1].name, lstep)
self.assertIsInstance(sim.transport_model, TransportModel)
self.assertIsInstance(sim.binding_model, BindingModel)
source_exp = sim.source_experiment
assert_has_traits_almost_equal(source_exp.column, sim.column)
self.assertIsNot(source_exp.column, sim.column)
if check_product:
assert_has_traits_almost_equal(source_exp.product, sim.product)