def test_execute___with_no_split_rows_not_looped___pipette_volumes_ok(
self):
# Arrange
builder = ExtensionBuilder.create_with_factor_extension()
builder.add_artifact_pair(source_vol=40,
dilute_factor=2,
target_vol=10)
builder.add_artifact_pair(source_vol=40,
dilute_factor=3,
target_vol=10)
builder.add_artifact_pair(source_conc=60,
source_vol=40,
dilute_factor=4,
target_vol=10)
# Act
builder.extension.execute()
# Assert
transfers = builder.transfers
self.assertEqual(5, transfers[0].pipette_sample_volume)
self.assertEqual(5, transfers[0].pipette_buffer_volume)
self.assertEqual(3.3, transfers[1].pipette_sample_volume)
self.assertEqual(6.7, transfers[1].pipette_buffer_volume)
self.assertEqual(2.5, transfers[2].pipette_sample_volume)
self.assertEqual(7.5, transfers[2].pipette_buffer_volume)
def test_run_execute__with_two_controls_and_one_normal_sample__examine_variables(
self):
# Arrange
builder = ExtensionBuilder.create_with_dna_extension()
builder.with_control_id_prefix("101C-")
builder.add_artifact_pair(source_container_name="source1")
builder.add_artifact_pair(source_container_name="control container",
is_control=True)
builder.add_artifact_pair(source_container_name="control container",
is_control=True)
# Act
builder.extension.execute()
# Assert
metadata_info = builder.metadata_info("Metadata filename",
HamiltonRobotSettings())
print_list(metadata_info.container_mappings, "container_mappings")
container_to_container_slot = metadata_info.transfer_batches[
0].container_to_container_slot
print_out_dict(container_to_container_slot.values(),
"Container to container slot")
print("Length of dict: {}".format(len(container_to_container_slot)))
print("Type that is mapped: {}".format(
type(container_to_container_slot[
container_to_container_slot.keys()[0]])))
self.assertEqual(1, 1)
def test_run_execute__with_two_previous_added_controls_and_one_normal__controls_included_in_container_mapping(
self):
"""
In this test, lims-id for control artifacts are updated with prefix 2-
"""
# Arrange
builder = ExtensionBuilder.create_with_dna_extension()
builder.with_control_id_prefix("2-")
builder.add_artifact_pair(source_container_name="source1")
builder.add_artifact_pair(source_container_name="control container",
is_control=True)
builder.add_artifact_pair(source_container_name="control container",
is_control=True)
# Act
builder.extension.execute()
# Assert
metadata_info = builder.metadata_info("Metadata filename",
HamiltonRobotSettings())
self.assertTrue(
"source1" in
[m[0].container.name for m in metadata_info.container_mappings])
self.assertTrue(
"control container" in
[m[0].container.name for m in metadata_info.container_mappings])
def test_execute___with_single_transfer_looped_dilution___exception_cast(
self):
# Arrange
builder = ExtensionBuilder.create_with_factor_extension()
builder.add_artifact_pair(source_vol=80,
dilute_factor=35,
target_vol=10)
# Act
# Assert
self.assertRaises(UsageError, lambda: builder.extension.execute())
def test_execute___with_one_transfer_lacking_dilute_factor___exception_cast(
self):
# Arrange
builder = ExtensionBuilder.create_with_factor_extension()
builder.add_artifact_pair(source_conc=10,
source_vol=10,
dilute_factor=None,
target_vol=40)
# Act
# Assert
self.assertRaises(UsageError, lambda: builder.extension.execute())
def test_execute___without_source_conc___target_conc_is_none(self):
# Arrange
builder = ExtensionBuilder.create_with_factor_extension()
builder.add_artifact_pair(source_vol=40,
dilute_factor=4,
target_vol=10)
# Act
builder.extension.execute()
# Assert
update_queue = list(builder.extension.context._update_queue)
output_artifact = update_queue[0]
self.assertIsNone(output_artifact.udf_dil_calc_target_conc)
def test_execute___with_split_row___updates_ok(self):
# Arrange
builder = ExtensionBuilder.create_with_factor_extension()
builder.add_artifact_pair(source_conc=80,
source_vol=80,
dilute_factor=10,
target_vol=80)
# Act
builder.extension.execute()
# Assert
output_artifact = builder.update_queue[0]
self.assertEqual(-9, output_artifact.udf_dil_calc_source_vol)
self.assertEqual(8, round(output_artifact.udf_dil_calc_target_conc, 1))
self.assertEqual(80, round(output_artifact.udf_dil_calc_target_vol, 1))
def test_execute___with_split_row___pipette_volume_ok(self):
# Arrange
builder = ExtensionBuilder.create_with_factor_extension()
builder.add_artifact_pair(source_conc=80,
source_vol=80,
dilute_factor=10,
target_vol=80)
# Act
builder.extension.execute()
# Assert
transfers = builder.transfers
self.assertEqual(2, len(transfers))
self.assertEqual(8, transfers[0].pipette_sample_volume)
self.assertEqual(36, transfers[0].pipette_buffer_volume)
self.assertEqual(0, transfers[1].pipette_sample_volume)
self.assertEqual(36, transfers[1].pipette_buffer_volume)
def test_execute___with_no_split_rows_not_looped___updates_ok(self):
# Arrange
builder = ExtensionBuilder.create_with_factor_extension()
builder.add_artifact_pair(source_conc=80,
source_vol=40,
dilute_factor=3,
target_vol=10)
# Act
builder.extension.execute()
# Assert
update_queue = list(builder.extension.context._update_queue)
output_artifact = update_queue[0]
self.assertEqual(1, len(update_queue))
self.assertEqual(-4.3, output_artifact.udf_dil_calc_source_vol)
self.assertEqual(26.7,
round(output_artifact.udf_dil_calc_target_conc, 1))
self.assertEqual(10, round(output_artifact.udf_dil_calc_target_vol))
def test_execute___with_one_transfer_exceeding_source_volume___warning(
self):
# Arrange
builder = ExtensionBuilder.create_with_factor_extension()
builder.add_artifact_pair(source_conc=10,
source_vol=10,
dilute_factor=3,
target_vol=40)
# Act
builder.extension.execute()
# Assert
self.assertEqual(
2,
builder.ext_wrapper.context_wrapper.
count_logged_validation_results_with_msg(
"Volume from sample exceeds current sample volume"))
def test_run_execute__with_two_added_controls_and_one_normal_sample__control_excluded_in_container_mappings(
self):
"""
container_mappings controls what is shown under source containers and target containers
in the xml metadata file
Negative controls are taken from the through and should not be included in the source
container list.
In future there will be a problem with several types of controls!
"""
# Arrange
builder = ExtensionBuilder.create_with_dna_extension()
builder.with_control_id_prefix("101C-")
builder.add_artifact_pair(source_container_name="source1")
builder.add_artifact_pair(source_container_name="control container",
is_control=True)
builder.add_artifact_pair(source_container_name="control container",
is_control=True)
# Act
builder.extension.execute()
# Assert
metadata_info = builder.metadata_info("Metadata filename",
HamiltonRobotSettings())
print_list(metadata_info.container_mappings, "container_mappings")
print_list(
[m[0].container.name for m in metadata_info.container_mappings],
"source containers in container_mappings")
self.assertTrue(
"source1" in
[m[0].container.name for m in metadata_info.container_mappings])
self.assertFalse(
"control container" in
[m[0].container.name for m in metadata_info.container_mappings])
def test_run_execute__with_two_controls_and_one_normal_sample__save_file_on_harddisk(
self):
# Arrange
builder = ExtensionBuilder.create_with_dna_extension()
builder.with_control_id_prefix("101C-")
builder.add_artifact_pair(source_container_name="source1")
builder.add_artifact_pair(source_container_name="control container",
is_control=True)
builder.add_artifact_pair(source_container_name="control container",
is_control=True)
# Act
builder.extension.execute()
# Arrange save to harddisk
artifact_service = builder.extension.context.artifact_service
upload_file_service = UploadFileService(
OSService(),
artifact_service=artifact_service,
disable_commits=True,
upload_dir=r"C:\Smajobb\2017\April\Run clarity\test_runs")
# Modified code taken from DilutionSession.execute()
today = datetime.date.today().strftime("%y%m%d")
metadata_file_handle = "Metadata"
metadata_files = list()
dilution_session = builder.extension.dilution_session
for robot in dilution_session.robot_settings:
metadata_file_name = "{}_{}_{}_{}.xml".format(
robot.name, today, "EE", "1234")
metadata_files.append((metadata_file_name,
builder.extension.generate_metadata_file(
robot, metadata_file_name)))
# Upload the metadata file:
upload_file_service.upload_files(metadata_file_handle, metadata_files)