def test_LabwareDefinition__get_cartesian_vector_to_top_of_well__raises_error_if_no_plate_height():
labware_definition = LabwareDefinition(
**copy_dict_with_key_removed(GENERIC_LABWARE_DEFINITION_KWARGS, "plate_height")
)
with pytest.raises(CartesianVectorRequirePlateHeightError):
labware_definition.get_cartesian_vector_to_top_of_well(
0, 0, CoordinateSystem(0, 0, 0, False)
)
def test_LabwareDefinition__validate_hash_components_calls_super__and_raises_error_if_invalid_id(
mocker,
):
spied_validate = mocker.spy(DomainModel, "validate_hash_components")
with pytest.raises(ValidationCollectionEmptyValueError) as e:
LabwareDefinition().validate_hash_components(autopopulate=False)
assert "uuid" in str(e)
assert spied_validate.call_count == 1
def test_LabwareDefinition__get_cartesian_vector_to_top_of_well(
labware_definition_kwargs,
row_idx,
col_idx,
coordinate_system,
function_call_kwargs,
expected_coordinates,
test_description,
):
labware_definition = LabwareDefinition(**labware_definition_kwargs)
actual_coordinates = labware_definition.get_cartesian_vector_to_top_of_well(
row_idx, col_idx, coordinate_system, **function_call_kwargs
)
assert actual_coordinates == expected_coordinates
def test_LabwareDefinition__create_portrait_definition__rotates_standard_96_well():
expected_plate_height = 14.2
expected_row_spacing = 9
expected_column_spacing = 9
landscape = LabwareDefinition(
row_count=8,
column_count=12,
plate_height=expected_plate_height,
row_center_to_center_spacing=expected_row_spacing,
column_center_to_center_spacing=expected_column_spacing,
)
portrait = landscape.create_portrait_definition()
assert portrait.row_count == 12
assert portrait.column_count == 8
assert portrait.plate_height == expected_plate_height
assert portrait.row_center_to_center_spacing == expected_row_spacing
assert portrait.column_center_to_center_spacing == expected_column_spacing
def test_LabwareDefinition__get_xy_coordinates_of_well__raises_error_if_definitions_missing(
labware_definition_kwargs,
row_idx,
col_idx,
function_call_kwargs,
expected_error,
test_description,
):
labware_definition = LabwareDefinition(**labware_definition_kwargs)
if expected_error is not None:
with pytest.raises(expected_error):
labware_definition.get_xy_coordinates_of_well(
row_idx, col_idx, **function_call_kwargs
)
else:
labware_definition.get_xy_coordinates_of_well(
row_idx, col_idx, **function_call_kwargs
)
def test_LabwareDefinition__get_xy_coordinates_of_well(
labware_definition_kwargs,
row_idx,
col_idx,
x_offset,
y_offset,
expected_coordinates,
test_description,
):
labware_definition = LabwareDefinition(**labware_definition_kwargs)
kwargs: Dict[str, Any] = dict()
if x_offset is not None:
kwargs["x_offset"] = x_offset
if y_offset is not None:
kwargs["y_offset"] = y_offset
actual_coordinates = labware_definition.get_xy_coordinates_of_well(
row_idx, col_idx, **kwargs
)
assert actual_coordinates == expected_coordinates
def test_LabwareDefinition__create_portrait_definition__rotates_agilent_8_row_trough():
expected_distance_to_liquid = 2
expected_row_spacing = (
9.01 # just to make it different than the 9 in the previous test
)
landscape = LabwareDefinition(
row_count=8,
center_of_a1=(14.29, 11.18),
distance_to_liquid=expected_distance_to_liquid,
row_center_to_center_spacing=expected_row_spacing,
)
portrait = landscape.create_portrait_definition()
assert portrait.row_count is None
assert portrait.column_count == 8
assert portrait.center_of_a1 == (11.18, 14.29)
assert portrait.distance_to_liquid == expected_distance_to_liquid
assert portrait.column_center_to_center_spacing == expected_row_spacing
assert portrait.row_center_to_center_spacing is None
def test_LabwareDefinition_validate_row_and_column_counts__raises_error_if_column_invalid():
m = LabwareDefinition(row_count=2, column_count="joe")
with pytest.raises(ValidationCollectionCannotCoerceError):
m.validate_row_and_column_counts()
GENERIC_UUID = uuid.UUID("3d118df7-3cb1-484e-85cd-b06def38bc91")
GENERIC_LABWARE_DEFINITION_KWARGS: Dict[str, Any] = {
"name": "12-well",
"uuid": GENERIC_UUID,
"row_count": 3,
"column_count": 4,
"center_of_a1": (8, 7),
"plate_height": 13.4,
"distance_to_liquid": 4,
"row_center_to_center_spacing": 12,
"column_center_to_center_spacing": 15,
}
GENERIC_LABWARE_DEFINITION = LabwareDefinition(
**GENERIC_LABWARE_DEFINITION_KWARGS)
GENERIC_LABWARE_DEFINITION_2 = LabwareDefinition(name="96-well",
uuid=GENERIC_UUID,
row_count=3,
column_count=4)
GENERIC_BARCODED_SBS_LABWARE_KWARGS = {
"uuid": GENERIC_UUID,
"barcode": "AB9938",
"labware_definition": GENERIC_LABWARE_DEFINITION_2,
}
GENERIC_BARCODED_SBS_LABWARE = BarcodedSbsLabware(
uuid=GENERIC_UUID,
barcode="AB9938",
def test_LabwareDefinition__get_row_and_column_from_well_index__raises_error_if_row_count_not_set():
labware_definition = LabwareDefinition(column_count=2)
with pytest.raises(
ValidationCollectionEmptyValueError, match="was empty row_count"
):
labware_definition.get_row_and_column_from_well_index(0)
def test_LabwareDefinition_autopopulate__fills_uuid():
m = LabwareDefinition()
m.autopopulate()
assert m.uuid is not None
m = LabwareDefinition(row_count="bob", column_count=12)
with pytest.raises(ValidationCollectionCannotCoerceError):
m.validate_row_and_column_counts()
def test_LabwareDefinition_validate_row_and_column_counts__raises_error_if_column_invalid():
m = LabwareDefinition(row_count=2, column_count="joe")
with pytest.raises(ValidationCollectionCannotCoerceError):
m.validate_row_and_column_counts()
@pytest.mark.parametrize(
"labware_definition,test_row,test_column,expected_error,test_description",
[
(
LabwareDefinition(row_count=2, column_count=2),
1,
2,
PositionInvalidForLabwareDefinitionError,
"column too high",
),
(
LabwareDefinition(row_count=2, column_count=2),
2,
1,
PositionInvalidForLabwareDefinitionError,
"row too high",
),
(
LabwareDefinition(row_count=2, column_count=2),
1,
}
)
CLOUD_API_ENDPOINT = (
f"api.{CLOUD_API_ENDPOINT_VALID_OPTIONS.get(CLOUD_API_ENDPOINT_USER_OPTION, 'curibio-test')}.com"
)
# Tanner (4/15/21): the latest HDF5 file version lives in mantarray-file-manager. This value represents the file version that is being created by the desktop app. When new mantarray-file-manager updates are brought into the desktop app, these values will differ indicating that FileWriterProcess needs to be updated to match the new file version
CURRENT_BETA1_HDF5_FILE_FORMAT_VERSION = "0.4.2"
CURRENT_BETA2_HDF5_FILE_FORMAT_VERSION = "1.0.1"
DEFAULT_SERVER_PORT_NUMBER = 4567
MAX_POSSIBLE_CONNECTED_BOARDS = 4
GENERIC_24_WELL_DEFINITION = LabwareDefinition(row_count=4, column_count=6)
FIRMWARE_VERSION_WIRE_OUT_ADDRESS = 0x21
BARCODE_SCANNER_TRIGGER_IN_ADDRESS = 0x41
BARCODE_SCANNER_TOP_WIRE_OUT_ADDRESS = 0x2A
BARCODE_SCANNER_MID_WIRE_OUT_ADDRESS = 0x2B
BARCODE_SCANNER_BOTTOM_WIRE_OUT_ADDRESS = 0x2C
CLEAR_BARCODE_TRIG_BIT = 0x5
START_BARCODE_SCAN_TRIG_BIT = 0x6
BARCODE_POLL_PERIOD = 15
BARCODE_CONFIRM_CLEAR_WAIT_SECONDS = 0.5
BARCODE_GET_SCAN_WAIT_SECONDS = 6
CLEARED_BARCODE_VALUE = chr(0) * 12
from pulse3D.constants import XEM_SERIAL_NUMBER_UUID
from pulse3D.plate_recording import WellFile
import pytest
from stdlib_utils import drain_queue
from stdlib_utils import invoke_process_run_and_check_errors
from stdlib_utils import TestingQueue
from .fixtures import GENERIC_STORED_CUSTOMER_ID
from .fixtures import QUEUE_CHECK_TIMEOUT_SECONDS
from .fixtures_mc_simulator import get_null_subprotocol
from .fixtures_mc_simulator import get_random_subprotocol
from .helpers import confirm_queue_is_eventually_empty
from .helpers import confirm_queue_is_eventually_of_size
from .helpers import put_object_into_queue_and_raise_error_if_eventually_still_empty
WELL_DEF_24 = LabwareDefinition(row_count=4, column_count=6)
GENERIC_ADC_OFFSET_VALUES: Dict[int, Dict[str, int]] = dict()
for this_well_idx in range(24):
GENERIC_ADC_OFFSET_VALUES[this_well_idx] = {
"construct": this_well_idx * 2,
"ref": this_well_idx * 2 + 1,
}
GENERIC_WELL_MAGNETOMETER_CONFIGURATION = {
channel_id: channel_id in (SERIAL_COMM_DEFAULT_DATA_CHANNEL,
SERIAL_COMM_SENSOR_AXIS_LOOKUP_TABLE["C"]["Z"])
for channel_id in range(SERIAL_COMM_NUM_DATA_CHANNELS)
}
GENERIC_NUM_CHANNELS_ENABLED = sum(
GENERIC_WELL_MAGNETOMETER_CONFIGURATION.values())
def test_LabwareDefinition__hash__hashes_uuid():
m = LabwareDefinition(uuid=GENERIC_UUID)
assert hash(m) == hash((GENERIC_UUID,))
def test_LabwareDefinition_super_is_called_during_init(mocker):
spied_init = mocker.spy(DomainModel, "__init__")
LabwareDefinition()
assert spied_init.call_count == 1
):
domain_model_validate_internals_test(
model,
attribute_under_test,
test_value,
additional_kwargs,
expected_error,
expected_texts_in_error,
)
@pytest.mark.parametrize(
"model1,model2,expected,test_description",
[
(
LabwareDefinition(row_count=8, column_count=12),
LabwareDefinition(),
False,
"empty vs something",
),
(
LabwareDefinition(
row_count=8, column_count=12, name="cool plate", uuid=GENERIC_UUID
),
LabwareDefinition(
row_count=8, column_count=12, name="cool plate", uuid=GENERIC_UUID
),
True,
"same everything",
),
(LabwareDefinition(row_count=8, column_count=12), 9, False, "different types"),