def setUp(self):
register_all_tree_node_adapters()
# Make a study and add all possible chromatography objects to the study
# Make a study with 1 experiment
self.study = make_sample_study(1)
simulation = make_sample_simulation()
self.study.simulations.append(simulation)
def setUp(self):
# Register all views
BaseModelViewTestCase.setUp(self)
# This could be the manual creation of an instance of the ChromData to
# represent.
self.model = make_sample_study()
def setUp(self):
self.datasource = SimpleDataSource()
proj_data = dict(study=make_blank_study(), datasource=self.datasource)
project = KromatographyProject(**proj_data)
self.task = KromatographyTask(project=project)
self.study2 = make_sample_study(num_exp=1)
proj_data = dict(study=self.study2, datasource=self.datasource)
project = KromatographyProject(**proj_data)
self.task2 = KromatographyTask(project=project)
def test_tree_node_adaptation(self):
register_all_tree_node_adapters()
study = make_sample_study()
data_manager = DataManager(data_elements=[study])
view = View(
Item('data_elements', editor=TreeEditor())
)
ui = data_manager.edit_traits(view=view)
ui.dispose()
def test_launch_app_for_study(self):
# Make a study, and launch the app around it
study = make_sample_study()
self.gui.invoke_after(STARTUP_TIME_MS, self.gui.stop_event_loop)
app = launch_app_for_study(study,
splash_screen_duration=0.,
confirm_on_window_close=False,
auto_close_empty_windows_on_open=True)
self.assertIn(study, app.initial_studies)
app.stop()
def setUp(self):
super(TestKromatographyTaskRunRequest, self).setUp()
self.datasource = SimpleDataSource()
self.task = KromatographyTask()
self.study2 = make_sample_study(num_exp=1)
project_data = dict(study=self.study2, datasource=self.datasource,
job_manager=self.job_manager)
project = KromatographyProject(**project_data)
self.task2 = KromatographyTask(project=project)
def load_study_with_exps_and_ran_sims():
""" Loads a study with two experiments and sims already ran.
DEPRECATED: use
kromatography.model.tests.sample_data_factories.make_sample_study instead.
"""
study = make_sample_study()
exp1, sim1 = load_default_experiment_simulation(expt_id='Run_1')
exp2, sim2 = load_default_experiment_simulation(expt_id='Run_2')
study.experiments = [exp1, exp2]
study.simulations = [sim1, sim2]
return study
def setUp(self):
self.standard_actions = [
DeleteAction, RenameAction, CopyAction, CutAction
]
register_all_tree_node_adapters()
# Make a study and add all possible chromatography objects to the study
# Make a study with 1 experiment
self.study = make_sample_study(1)
simulation = make_sample_simulation()
self.study.simulations.append(simulation)
self.user_ds = make_sample_user_ds(with_bind_trans=True)
self.user_ds_entries = self.user_ds.object_catalog.keys()
self.user_ds_objects = [
getattr(self.user_ds, key) for key in self.user_ds_entries
]
self.study.study_datasource.binding_models.\
append(self.study.simulations[0].binding_model)
self.study.study_datasource.transport_models.\
append(self.study.simulations[0].transport_model)
in_study_ds = self.study.study_datasource
self.in_study_ds_entries = in_study_ds.object_catalog.keys()
self.in_study_objects = [
getattr(in_study_ds, key) for key in self.in_study_ds_entries
]
def test_StudyDataSourceEntryCreator(self):
study = make_sample_study()
for key in STUDY_DATASOURCE_OBJECT_FACTORIES:
creator = StudyDataSourceEntryCreator(study=study,
datasource_key=key)
self.assertCreatorValid(creator, key)
def test_prepare_study_datasource_catalog(self):
study = make_sample_study()
prepare_study_datasource_catalog(study)
ds = study.study_datasource
self.assertCreatorOnAllEntries(ds)
def setUp(self):
self.model = make_sample_study()
self.klass = Study
def setUp(self):
register_all_tree_node_adapters()
self.study = make_sample_study()
self.model = make_sample_simulation()
self.study.simulations.append(self.model)
def setUp(self):
BaseStudyTestCase.setUp(self)
self.study_class = Study
self.study = make_sample_study()
self.constructor_data = STUDY_DATA
def _get_can_create(self):
can_create = self.experiment_selected and self.transport_model and \
self.binding_model
return can_create
def generate_sim_names(expt_names, study):
""" Generate a list of simulation names for experiment names provided which
are not already present in the study's existing simulations.
"""
names = []
existing_sim_names = [sim.name for sim in study.simulations]
for expt in expt_names:
candidate = generate_sim_name(expt)
candidate = add_suffix_if_exists(candidate, existing_sim_names)
names.append(candidate)
return names
if __name__ == "__main__":
from kromatography.model.tests.sample_data_factories import \
make_sample_study
study = make_sample_study(num_exp=5)
sim_builder = SimulationFromExperimentBuilder(
experiment_selector=ExperimentSelector(study=study),
target_study=study,
)
sim_builder.configure_traits()
print("selected: {}".format(sim_builder.experiment_selected))
def setUp(self):
GuiTestAssistant.setUp(self)
self.study2 = make_sample_study(num_exp=1)
def _get_column(self):
return self._get_object_clone_from_name("columns", self.column_name)
def _get_product(self):
return self._get_object_clone_from_name("products", self.product_name)
def _get_method(self):
if self.method_name:
method = self._get_object_clone_from_name("methods",
self.method_name)
method.initial_buffer = self.initial_buffer
return method
def _get_step_names(self):
if self.method_name:
return [step.name for step in self.method.method_steps]
else:
return []
if __name__ == "__main__":
from kromatography.model.data_source import SimpleDataSource
from kromatography.model.tests.sample_data_factories import \
make_sample_study
study = make_sample_study()
sim_builder = SimulationFromDatasourceBuilder(
datasource=SimpleDataSource(), study_datasource=study.study_datasource
)
sim_builder.configure_traits()
from unittest import TestCase
from traits.testing.unittest_tools import UnittestTools
from app_common.traits.assertion_utils import assert_has_traits_almost_equal
from kromatography.ui.simulation_from_experiment_builder import \
generate_sim_names, SimulationFromExperimentBuilder
from kromatography.model.factories.simulation import generate_sim_name
from kromatography.model.tests.sample_data_factories import \
make_sample_study, make_sample_study2
from kromatography.ui.experiment_selector import ExperimentSelector
from kromatography.model.api import BindingModel, Buffer, Method, \
Simulation, TransportModel
STUDY = make_sample_study(num_exp=5)
class TestGenerateSimNames(TestCase):
def test_1_name(self):
self.assertIsInstance(generate_sim_name("Run 1"), str)
self.assertIsInstance(generate_sim_name("Run_1"), str)
def test_n_names(self):
names = generate_sim_names(["Run 1", "Run 2"], STUDY)
self.assertIsInstance(names, list)
for name in names:
self.assertIsInstance(name, str)
class TestSimulationFromExperimentBuilder(TestCase, UnittestTools):
@classmethod
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,
)
