def test_invalid_container_name():
if ff.split_labware_definitions():
error_type = FileNotFoundError
else:
error_type = ValueError
with pytest.raises(error_type):
database.load_container("fake_container")
def test_labware_create(dummy_db):
from opentrons import labware
lw_name = '15-well-plate'
if lw_name in labware.list():
database.delete_container(lw_name)
n_cols = 5
n_rows = 3
col_space = 12
row_space = 18
diameter = 5
height = 20
volume = 3.14 * (diameter / 2.0)**2
res = labware.create(lw_name, (n_cols, n_rows), (col_space, row_space),
diameter, height, volume)
lw = database.load_container(lw_name)
database.delete_container(lw_name)
assert len(lw.wells()) is n_cols * n_rows
for well in lw.wells():
name = well.get_name()
assert res[name].coordinates() == well.coordinates()
for prop in ['height', 'diameter']:
assert res[name].properties[prop] == well.properties[prop]
assert lw.well("B5").coordinates() == ((n_cols - 1) * col_space, row_space,
0)
assert lw.well("C3").coordinates() == (2 * col_space, 0, 0)
assert lw.well(2).get_name() == 'C1'
def _setup_container(container_name):
try:
container = database.load_container(container_name)
# Database.load_container throws ValueError when a container name is not
# found.
except ValueError:
# First must populate "get persisted container" list
old_container_loading.load_all_containers_from_disk()
# Load container from old json file
container = old_container_loading.get_persisted_container(
container_name)
# Rotate coordinates to fit the new deck map
rotated_container = database_migration.rotate_container_for_alpha(
container)
# Save to the new database
database.save_new_container(rotated_container, container_name)
container.properties['type'] = container_name
container_x, container_y, container_z = container._coordinates
if not fflags.split_labware_definitions():
# infer z from height
if container_z == 0 and 'height' in container[0].properties:
container_z = container[0].properties['height']
from opentrons.util.vector import Vector
container._coordinates = Vector(container_x, container_y, container_z)
return container
def test_load_persisted_container():
plate = database.load_container("24-vial-rack")
assert isinstance(plate, Container)
assert isinstance(plate, Container)
assert all([isinstance(w, Well) for w in plate])
assert plate[0].coordinates() == (8.19, 63.76, 0)
assert plate['A2'].coordinates() == (27.49, 63.76, 0)
def test_seralizer_all_containers():
new_defs = ['opentrons-tiprack-300ul', 'tube-rack-5ml-96', '4-well-plate']
plates = [item for item in ldef.list_all_labware() if item not in new_defs]
for plate in plates:
old_container = sqldb.load_container(plate)
json_from_file = ldef._load_definition(test_defn_root, plate)
json_from_container = ser.container_to_json(old_container)
assert json_from_container['ordering'] == json_from_file['ordering']
assert json_from_container['wells'] == json_from_file['wells']
def test_load_persisted_container(robot):
plate = database.load_container("96-flat")
assert isinstance(plate, Container)
assert isinstance(plate, Container)
assert all([isinstance(w, Well) for w in plate])
offset_x = 11.24
offset_y = 14.34
width = 85.48
well_a1 = (offset_y, width - offset_x, 0)
well_d6 = (offset_y + 45, width - (offset_x + 27), 0)
assert plate[0].coordinates() == well_a1
assert plate['D6'].coordinates() == well_d6
def test_one_serializer():
plate = '6-well-plate'
old_container = sqldb.load_container(plate)
json_from_file = ldef._load_definition(test_defn_root, plate)
json_from_container = ser.container_to_json(old_container)
# Metadata comparison does not work in test, because the constructed
# Container does not have a parent, and Container does not keep track of
# its own name--the name is saved by the parent, so
# new_json['metadata']['name'] in this test will be None
assert json_from_container['ordering'] == json_from_file['ordering']
assert json_from_container['wells'] == json_from_file['wells']
def test_one_deserializer():
plate = '6-well-plate'
new_container = ser.json_to_container(
ldef._load_definition(test_defn_root, plate))
old_container = sqldb.load_container(plate)
old_wells = {
wellname: [
round(well._coordinates[i] + old_container._coordinates[i], 3)
for i in [0, 1, 2]
]
for wellname, well in old_container.children_by_name.items()
}
new_wells = {
wellname: [well._coordinates[i] for i in [0, 1, 2]]
for wellname, well in new_container.children_by_name.items()
}
assert old_wells == new_wells
def create(name, grid, spacing, diameter, depth, volume=0):
"""
Creates a labware definition based on a rectangular gird, depth, diameter,
and spacing. Note that this function can only create labware with regularly
spaced wells in a rectangular format, of equal height, depth, and radius.
Irregular labware defintions will have to be made in other ways or modified
using a regular definition as a starting point. Also, upon creation a
definition always has its lower-left well at (0, 0, 0), such that this
labware _must_ be calibrated before use.
:param name: the name of the labware to be used with `labware.load`
:param grid: a 2-tuple of integers representing (<n_columns>, <n_rows>)
:param spacing: a 2-tuple of floats representing
(<col_spacing, <row_spacing)
:param diameter: a float representing the internal diameter of each well
:param depth: a float representing the distance from the top of each well
to the internal bottom of the same well
:param volume: [optional] the maximum volume of each well
:return: the labware object created by this function
"""
columns, rows = grid
col_spacing, row_spacing = spacing
custom_container = Container()
properties = {
'type': 'custom',
'diameter': diameter,
'height': depth,
'total-liquid-volume': volume
}
for r in range(rows):
for c in range(columns):
well = Well(properties=properties)
well_name = chr(r + ord('A')) + str(1 + c)
coordinates = (c * col_spacing, (rows - r - 1) * row_spacing, 0)
custom_container.add(well, well_name, coordinates)
database.save_new_container(custom_container, name)
return database.load_container(name)
def test_invalid_container_name(robot):
error_type = ValueError
with pytest.raises(error_type):
database.load_container("fake_container")