def test_UserDataSourceEntryCreator(self):
datasource = SimpleDataSource()
for key in DATASOURCE_OBJECT_FACTORIES:
creator = UserDataSourceEntryCreator(
datasource=datasource, datasource_key=key
)
self.assertCreatorValid(creator, key)
def setUp(self):
GuiTestAssistant.setUp(self)
register_all_data_views()
datasource = SimpleDataSource()
product = datasource.get_object_of_type("products", 'Prod001')
ds = InStudyDataSource()
buf = Buffer(**BUFFER_ELUTION)
ds.set_object_of_type("buffers", buf)
self.study = Study(name="test",
product=product,
datasource=datasource,
study_datasource=ds)
ds = InStudyDataSource()
self.study2 = Study(name="test2",
datasource=datasource,
study_datasource=ds)
def test_read_input_files_with_release_ds(self):
ds = SimpleDataSource.from_data_catalog(DATA_CATALOG)
# Make sure that's the external datasource
self.assertEqual(len(ds.products), 3)
study = load_study_from_excel(self.tutorial_file,
datasource=ds,
allow_gui=False)
self.assert_valid_tutorial_study(study)
def test_read_input_files_with_internal_ds(self):
ds = SimpleDataSource()
# Make sure that's the internal datasource
self.assertGreater(len(ds.products), 5)
study = load_study_from_excel(self.tutorial_file,
datasource=ds,
allow_gui=False)
self.assert_valid_tutorial_study(study)
class TestProductChooser(TestCase):
def setUp(self):
self.ds = SimpleDataSource()
self.prod_chooser = ProductChooser(datasource=self.ds)
def test_create_ui(self):
ui = self.prod_chooser.edit_traits()
ui.dispose()
def test_selection(self):
target_prod = self.ds.get_object_names_by_type("products")[0]
self.prod_chooser.selected_product_name = target_prod
expected = self.ds.get_object_of_type("products", target_prod)
assert_has_traits_almost_equal(self.prod_chooser.selected_product,
expected)
assert (self.prod_chooser.selected_product is not expected)
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 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)
class TestHighLevelFileStorageDataSource(TestCaseWithTempFile):
""" Test of high level functions save_object and load_object on
SimpleDatasource instances.
"""
def setUp(self):
super(TestHighLevelFileStorageDataSource, self).setUp()
self.ds = SimpleDataSource()
def test_default_simple_datasource(self):
assert_file_roundtrip_identical(self.ds)
def test_modified_simple_datasource_via_list(self):
# FIXME: adding to the datasource currently means adding to the
# object_catalog, to the data catalog and the corresponding list
new_comp = Component(name="New Component",
charge=UnitScalar(0.0, units='1'),
pKa=UnitScalar(0.0, units='1'))
self.ds.set_object_of_type("components", new_comp)
self.ds.make_clean()
assert_file_roundtrip_identical(self.ds)
def make_sample_user_ds(with_bind_trans=False, num_comp=4):
""" Make a sample User datasource, optionally adding a sample binding and
transport models to the data catalog content.
"""
user_ds = SimpleDataSource()
if with_bind_trans:
# Add a sample binding and transport models to test their adaptation
sample_bind_model = make_sample_binding_model(num_comp)
user_ds.binding_models.append(sample_bind_model)
sample_transp_model = make_sample_transport_model(num_comp)
user_ds.transport_models.append(sample_transp_model)
return user_ds
def load_default_user_datasource():
""" Load or build the default user datasource.
If a datasource was stored in the default, location, load the newest one.
Otherwise, build a new SimpleDataSource.
Returns
-------
tuple with a SimpleDatasource instance and the file if any that it was
loaded from.
"""
from kromatography.model.data_source import SimpleDataSource
from kromatography.io.reader_writer import load_object
# Logger defined here so that the logger can be defined after the
# initialize_logging is called.
logger = logging.getLogger(__name__)
last_stored_ds_file = get_newest_app_file(extension=DS_EXT)
if last_stored_ds_file is not None:
try:
ds, legacy_file = load_object(last_stored_ds_file)
msg = "Loaded datasource from {}".format(last_stored_ds_file)
logger.info(msg)
if legacy_file:
msg = "Datasource storage {} is a legacy file."
logger.info(msg)
except Exception as e:
msg = ("Failed to load the last datasource file {}. The file "
"might be corrupted, and mights need to be removed. Error "
"was {}.").format(last_stored_ds_file, e)
logger.error(msg)
last_stored_ds_file = None
# Not doing an else, so that this is executed when exception raised:
if last_stored_ds_file is None:
msg = "No valid datasource file found. Loading a default one."
logger.debug(msg)
ds = SimpleDataSource(name="User DataSource")
last_stored_ds_file = ""
return ds, last_stored_ds_file
def test_prepare_datasource_catalog(self):
datasource = SimpleDataSource()
prepare_datasource_catalog(datasource)
self.assertCreatorOnAllEntries(datasource)
def setUp(self):
# Regist the views
BaseModelViewTestCase.setUp(self)
s = SimpleDataSource()
self.model = s.get_object_of_type('chemicals', 'Sodium_Acetate')
class TestSimulationBuilderDialog(TestCase):
def setUp(self):
self.datasource = SimpleDataSource()
self.study = make_sample_study2(add_transp_bind_models=True)
self.study_ds = self.study.study_datasource
self.sim_builder = SimulationFromDatasourceBuilder(
datasource=self.datasource, study_datasource=self.study_ds)
def test_bring_up(self):
ui = self.sim_builder.edit_traits()
ui.dispose()
def test_product_selection(self):
target_prod = self.datasource.get_object_names_by_type("products")[0]
self.sim_builder.product_name = target_prod
exp = self.datasource.get_object_of_type("products", target_prod)
assert_has_traits_almost_equal(self.sim_builder.product, exp)
def test_build_simulation(self):
# Setup
self.sim_builder.column_name = 'CP_001'
self.sim_builder.method_name = 'Run_1'
self.sim_builder.first_simulated_step_name = 'Load'
self.sim_builder.last_simulated_step_name = 'Strip'
self.sim_builder.transport_model_name = DEFAULT_TRANSPORT_MODEL_NAME
self.sim_builder.binding_model_name = DEFAULT_BINDING_MODEL_NAME
sim = self.sim_builder.to_simulation()
self.assertIsInstance(sim, Simulation)
# init buffer:
self.assertEqual(self.sim_builder.initial_buffer_name, '')
exp1 = self.study.search_experiment_by_name("Run_1")
equil_buffer = exp1.method.method_steps[1].solutions[0].name
self.assertEqual(sim.method.initial_buffer.name, equil_buffer)
# the simulation has to be valid enough that it can be converted to a
# CADET input...
cadet_input = build_cadet_input(sim)
self.assertIsInstance(cadet_input, CADETInput)
def test_build_simulation_force_init_buffer(self):
# Setup
self.sim_builder.column_name = 'CP_001'
self.sim_builder.method_name = 'Run_1'
self.sim_builder.first_simulated_step_name = 'Load'
self.sim_builder.last_simulated_step_name = 'Strip'
self.sim_builder.initial_buffer_name = 'Elution_1'
self.sim_builder.transport_model_name = DEFAULT_TRANSPORT_MODEL_NAME
self.sim_builder.binding_model_name = DEFAULT_BINDING_MODEL_NAME
sim = self.sim_builder.to_simulation()
self.assertIsInstance(sim, Simulation)
self.assertEqual(sim.method.initial_buffer.name, 'Elution_1')
def test_change_method_name_changes_first_last_guesses(self):
self.assertIsNone(self.sim_builder.first_simulated_step_name)
self.assertIsNone(self.sim_builder.last_simulated_step_name)
self.sim_builder.method_name = 'Run_1'
self.assertEqual(self.sim_builder.first_simulated_step_name,
'Pre-Equilibration')
self.assertEqual(self.sim_builder.last_simulated_step_name, 'Strip')
def test_change_method_changes_solution_list(self):
self.sim_builder.method_name = 'Run_1'
all_solutions = []
for step in self.sim_builder.method.method_steps:
all_solutions += [
sol.name for sol in step.solutions if isinstance(sol, Buffer)
]
# Sim builder also allows the init_buffer to be blank so that it is
# looked up in the source experiment:
all_solutions += [""]
self.assertEqual(set(all_solutions), set(self.sim_builder.all_buffers))
def setUp(self):
self.datasource = SimpleDataSource()
self.study = make_sample_study2(add_transp_bind_models=True)
self.study_ds = self.study.study_datasource
self.sim_builder = SimulationFromDatasourceBuilder(
datasource=self.datasource, study_datasource=self.study_ds)
def setUp(self):
# Regist the views
BaseModelViewTestCase.setUp(self)
s = SimpleDataSource()
self.model = s.get_object_of_type('components', 'Acetate')
)
return view
# -------------------------------------------------------------------------
# Traits listeners
# -------------------------------------------------------------------------
@on_trait_change("model.product_component_assays[]")
def get_product_component_assays(self):
assay_names = self.model.product_component_assays
self.product_component_assays = assay_instances_from_names(assay_names)
@on_trait_change("product_component_assays, product_component_assays.name,"
"product_component_assays[]")
def update_model_product_component_assays(self):
self.model.product_component_assays = assay_names_from_instances(
self.product_component_assays)
if __name__ == '__main__':
from kromatography.model.data_source import SimpleDataSource
from kromatography.utils.app_utils import initialize_unit_parser
initialize_unit_parser()
s = SimpleDataSource()
product = s.get_object_of_type('products', 'Prod001')
product_view = ProductView(model=product)
product_view.configure_traits()
product.print_traits()
def setUp(self):
self.ds = SimpleDataSource()
self.builder = ProductBuilder(datasource=self.ds)
def build_chemical_component_table_editor(known_component_names):
""" Build an editor for a list of chemical components.
"""
default_count = 1
component_editor = TableEditor(
columns=[
ObjectColumn(name='name',
editor=EnumEditor(values=known_component_names)),
ObjectColumn(name='component_atom_count')
],
editable=True,
sortable=False,
deletable=True,
row_factory=ChemicalComponent,
row_factory_kw={
"name": known_component_names[0],
"component_atom_count": default_count
},
)
return component_editor
if __name__ == '__main__':
# setting up model
from kromatography.model.data_source import SimpleDataSource
s = SimpleDataSource()
model = s.build_chemical_from_data("Sodium_Chloride")
model_view = ChemicalView(model=model)
model_view.configure_traits()
solution.chemical_component_concentrations = UnitArray(
[comp.concentration[()] for comp in chem_comps],
units=comp.concentration.units
)
else:
solution.chemical_component_concentrations = UnitArray([])
# Traits property getters/setters -----------------------------------------
def _get__has_strip(self):
return STRIP_COMP_NAME in self.model.product.product_component_assays
def __strip_desc_default(self):
strip_desc = r"The strip fraction describes the percentage of total " \
r"absorbance to assign to the strip component. (Use " \
r"the dedicated tool to modify: <i>Tools > {}</i>.)"
strip_desc = strip_desc.format(STRIP_TOOL_NAME)
return strip_desc
if __name__ == '__main__':
# setting up model
from kromatography.model.tests.example_model_data import SOLUTIONWITHPRODUCT_LOAD # noqa
from kromatography.model.data_source import SimpleDataSource
ds = SimpleDataSource()
solution = SolutionWithProduct(**SOLUTIONWITHPRODUCT_LOAD)
solution.print_traits()
solution_view = SolutionWithProductView(model=solution, datasource=ds)
solution_view.configure_traits()
class TestProductBuilder(TestCase):
def setUp(self):
self.ds = SimpleDataSource()
self.builder = ProductBuilder(datasource=self.ds)
def test_bring_up(self):
self.builder.expert_mode = False
with temp_bringup_ui_for(self.builder):
pass
self.builder.expert_mode = True
with temp_bringup_ui_for(self.builder):
pass
def test_default_attributes(self):
self.assertFalse(self.builder.expert_mode)
# Default target product not known in default datasource
known_products = {comp.target_product for comp in
self.ds.get_objects_by_type("product_components")}
self.assertNotIn(self.builder.name, known_products)
# Therefore, there are no candidate components:
self.assertEqual(self.builder._component_candidates_names, [])
def test_build_product_fail_no_type(self):
prod = self.builder.build_product(allow_ui=False)
self.assertIsNone(prod)
def test_build_product_empty_default(self):
self.builder.product_type = "Globular"
prod = self.builder.build_product(allow_ui=False)
self.assertIsInstance(prod, Product)
self.assertEqual(len(prod.product_components), 1)
comp = prod.product_components[0]
self.assertEqual(comp.name, STRIP_COMP_NAME)
self.assertEqual(comp.target_product, prod.name)
def test_build_product_empty_no_strip(self):
self.builder.product_type = "Globular"
self.builder.add_strip = False
prod = self.builder.build_product(allow_ui=False)
self.assertIsInstance(prod, Product)
self.assertEqual(prod.product_components, [])
def test_build_product_empty_expert_mode(self):
self.builder.product_type = "Globular"
self.builder.expert_mode = True
prod = self.builder.build_product(allow_ui=False)
self.assertIsInstance(prod, Product)
self.assertEqual(prod.product_components, [])
def test_build_product_with_comp_expert_mode(self):
""" Test that builder in expert mode can rebuild PROD000.
"""
original_prod0 = self.ds.get_objects_by_type("products",
{"name": "Prod000"})[0]
comp_names = [c.name for c in original_prod0.product_components]
self.builder.name = "Prod000"
self.builder.product_type = "Globular"
self.builder.pI = UnitScalar(7.52, units='1')
self.builder.expert_mode = True
# In expert mode, we set the list of assay names and component names
# and expressions:
for name in comp_names:
assay_name = "CEX_{}".format(name)
exp = "product_concentration * {} / 100".format(assay_name)
comp_desc = ComponentDescription(name=name,
concentration_exps=exp)
self.builder.component_descs.append(comp_desc)
assay = ProductComponentAssay(name=assay_name)
self.builder.component_assay_names.append(assay)
prod = self.builder.build_product(allow_ui=False)
ignore = ["amino_acids", "amino_acid_numbers"]
assert_has_traits_almost_equal(prod, original_prod0,
ignore=ignore)
# In expert mode, add_strip is ignored:
self.builder.add_strip = True
prod = self.builder.build_product(allow_ui=False)
ignore = ["amino_acids", "amino_acid_numbers"]
assert_has_traits_almost_equal(prod, original_prod0,
ignore=ignore)
def test_build_product_with_comp_simplified_mode(self):
""" Modify PROD000 and make sure builder can rebuild it (no strip).
Simplify its component and assay names, and make sure the simplified
builder with add_strip=False can rebuild it.
"""
orig_prod0 = self.ds.get_objects_by_type("products",
{"name": "Prod000"})[0]
comp_names = [c.name for c in orig_prod0.product_components]
# Change the assays to be named like the components since the
# simplified mode only supports that:
orig_assays = ['CEX_Acidic_2', 'CEX_Acidic_1', 'CEX_Native']
self.assertEqual(orig_prod0.product_component_assays, orig_assays)
orig_prod0.product_component_assays = comp_names
exps = ["product_concentration * CEX_{} / 100".format(name)
for name in comp_names]
orig_conc_exps = Series(exps, index=comp_names)
assert_series_equal(orig_prod0.product_component_concentration_exps,
orig_conc_exps)
new_exps = ["product_concentration * {} / 100".format(name)
for name in comp_names]
orig_prod0.product_component_concentration_exps = \
Series(new_exps, index=comp_names)
self.builder.name = "Prod000"
self.builder.product_type = "Globular"
self.builder.pI = UnitScalar(7.52, units='1')
self.builder.expert_mode = False
self.builder.add_strip = False
# In simplified mode, we just set a list of component names:
for name in comp_names:
comp_desc = ComponentDescription(name=name)
self.builder.component_descs.append(comp_desc)
prod = self.builder.build_product(allow_ui=False)
ignore = ["amino_acids", "amino_acid_numbers"]
assert_has_traits_almost_equal(prod, orig_prod0,
ignore=ignore)
def test_build_product_with_comp_simplified_mode_with_strip(self):
""" Modify PROD000 and make sure builder can rebuild it (with strip).
Add a strip to it, and change its component and assay names, and make
sure the simplified building with the add_strip=True.
"""
orig_prod0 = self.ds.get_objects_by_type("products",
{"name": "Prod000"})[0]
comp_names = [c.name for c in orig_prod0.product_components]
# Change the assays to be named like the components since the
# simplified mode only supports that:
orig_prod0.product_component_assays = comp_names
new_exps = ["product_concentration * {} / 100".format(name)
for name in comp_names]
orig_prod0.product_component_concentration_exps = \
Series(new_exps, index=comp_names)
# Modify the prod to add a strip
new_prod, strip_comp = add_strip_to_product(orig_prod0)
# Rebuild prod0 with the builder:
self.builder.name = new_prod.name
self.builder.product_type = "Globular"
self.builder.pI = UnitScalar(7.52, units='1')
self.builder.expert_mode = False
self.builder.add_strip = True
for comp in new_prod.product_components:
name = comp.name
if name != STRIP_COMP_NAME:
self.ds.set_object_of_type("product_components", comp)
comp_desc = ComponentDescription(name=name)
self.builder.component_descs.append(comp_desc)
prod = self.builder.build_product(allow_ui=False)
ignore = ["amino_acids", "amino_acid_numbers", "name"]
assert_has_traits_almost_equal(prod, new_prod, ignore=ignore)
def setUp(self):
super(TestHighLevelFileStorageDataSource, self).setUp()
self.ds = SimpleDataSource()
def setUp(self):
self.ds = SimpleDataSource.from_data_catalog(data_catalog=DATA_CATALOG)
"""
columns = [ObjectColumn(name='name', style="readonly",
label="Component name",
tooltip="Name of component to build product with. "
"Must exist in user data.")]
if expert_mode:
tooltip = ("Enter the expression to compute the component's "
"concentration, as a function of the total product "
"concentration ('product_concentration') and the component "
"assay names.")
columns += [ObjectColumn(name='concentration_exps',
label="Component concentration expression",
tooltip=tooltip)]
editor = TableEditor(
columns=columns,
editable=True,
sortable=False,
deletable=True,
)
return editor
if __name__ == "__main__":
logging.basicConfig(level=logging.DEBUG)
builder = ProductBuilder(datasource=SimpleDataSource())
builder.configure_traits()
builder.build_product()
def _datasource_default(self):
return SimpleDataSource()
def setUp(self):
self.ds = SimpleDataSource()
self.prod_chooser = ProductChooser(datasource=self.ds)
def setUp(self):
self.datasource = SimpleDataSource()
self.task = KromatographyTask()
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()
