def test_size_of_load_experimental_request(self):
experimental_request = ExperimentalRequest(
ip_constants.AQUARIUM_NAMESPACE, self.opil_lab_template, 'foo_id',
'IntentParserCopy_foo', 'https://docs.google.com/document/d/foo')
experimental_request.load_experimental_request()
self.assertEqual(1,
len(experimental_request.opil_experimental_requests))
def test_size_of_load_sampleset_template_from_protocol_interface(self):
experimental_request = ExperimentalRequest(
ip_constants.AQUARIUM_NAMESPACE, self.opil_lab_template, 'foo_id',
'IntentParserCopy_foo', 'https://docs.google.com/document/d/foo')
experimental_request.load_sample_template_from_protocol_interface()
self.assertIsNotNone(experimental_request.sample_template)
self.assertEqual('http://aquarium.bio/htc_design',
experimental_request.sample_template.identity)
def test_experimental_reference_url_annotation(self):
experimental_request = ExperimentalRequest(
ip_constants.AQUARIUM_NAMESPACE, self.opil_lab_template, 'foo_id',
'IntentParserCopy_foo', 'https://docs.google.com/document/d/foo')
experimental_request.load_experimental_request()
self.assertEqual(
'https://docs.google.com/document/d/foo', experimental_request.
opil_experimental_requests[0].experiment_reference_url)
def test_size_of_sample_sets(self):
experimental_request = ExperimentalRequest(
ip_constants.AQUARIUM_NAMESPACE, self.opil_lab_template, 'foo_id',
'IntentParserCopy_foo', 'https://docs.google.com/document/d/foo')
measurement_table = MeasurementTable(
self._create_dummy_measurement_table())
measurement_table.process_table()
experimental_request.load_from_measurement_table(measurement_table)
experimental_request.load_sample_template_from_protocol_interface()
experimental_request.create_subcomponents_from_template()
experimental_request.load_sample_set(
len(measurement_table.get_intents()))
self.assertEqual(2, len(experimental_request.opil_sample_sets))
def test_for_original_sample_set_by_identity(self):
experimental_request = ExperimentalRequest(
ip_constants.AQUARIUM_NAMESPACE, self.opil_lab_template, 'foo_id',
'IntentParserCopy_foo', 'https://docs.google.com/document/d/foo')
measurement_table = MeasurementTable(
self._create_dummy_measurement_table())
measurement_table.process_table()
experimental_request.load_from_measurement_table(measurement_table)
experimental_request.load_sample_template_from_protocol_interface()
experimental_request.create_subcomponents_from_template()
experimental_request.load_sample_set(
len(measurement_table.get_intents()))
actual_sample_set_identities = [
sample.identity for sample in experimental_request.opil_sample_sets
]
self.assertTrue('http://aquarium.bio/culture_conditions' in
actual_sample_set_identities)
def test_subcomponent_names(self):
experimental_request = ExperimentalRequest(
ip_constants.AQUARIUM_NAMESPACE, self.opil_lab_template, 'foo_id',
'IntentParserCopy_foo', 'https://docs.google.com/document/d/foo')
measurement_table = MeasurementTable(
self._create_dummy_measurement_table())
measurement_table.process_table()
experimental_request.load_from_measurement_table(measurement_table)
experimental_request.load_sample_template_from_protocol_interface()
experimental_request.create_subcomponents_from_template()
expected_subcomponent_names = [
'Antibiotic', 'Inducer', 'Media', 'Strain'
]
for feature in experimental_request.sample_template.features:
self.assertTrue(feature.name in expected_subcomponent_names)
def _process_opil(self):
if not self.processed_protocol_name:
raise IntentParserException(
'Name of lab must be provided for describing an experimental request but'
'none was given.')
opil_lab_template = self._lab_protocol_accessor.load_protocol_interface_from_lab(
self.processed_protocol_name, self.processed_lab_name)
experiment_id = self.processed_lab.to_structured_request()[
dc_constants.EXPERIMENT_ID]
experimental_request = ExperimentalRequest(
self._get_namespace_from_lab(), opil_lab_template, experiment_id,
self._experiment_ref, self._experiment_ref_url)
experimental_request.load_experimental_request()
# add control table info
if self.processed_controls:
for control_table in self.processed_controls.values():
experimental_request.load_from_control_table(control_table)
# add measurement table info
if self.measurement_table:
experimental_request.load_from_measurement_table(
self.measurement_table)
experimental_request.load_sample_template_from_protocol_interface()
experimental_request.create_subcomponents_from_template()
experimental_request.load_sample_set(
len(self.measurement_table.get_intents()))
experimental_request.add_variable_features_from_measurement_intents(
self.measurement_table.get_intents())
experimental_request.load_and_update_measurement(
self.measurement_table.get_intents())
# add parameter table info
if self.processed_parameter:
experimental_request.load_lab_parameters()
experimental_request.update_parameter_values(
self.processed_parameter.get_default_parameters())
experimental_request.add_run_parameters(self.processed_parameter)
experimental_request.connect_properties()
self.opil_document = experimental_request.to_opil()