def test_instr_max_height():
deck = Deck()
trough = labware.load(trough_name, deck.position_for(1))
trough2 = labware.load(trough_name, deck.position_for(2))
deck[1] = trough
deck[2] = trough2
# if the highest deck height is between 1 mm and 10 mm below
# the max instrument achievable height, we use the max instrument
# height as the safe height
instr_max_height = trough.wells()[0].top().point.z + 1
height = safe_height(
trough.wells()[0].top(), trough2.wells()[0].top(),
deck, round(instr_max_height, 2), 7.0, 15.0)
assert height == round(instr_max_height, 2)
# if the highest deck height is > 10 mm below the max instrument
# height, we use the lw_z_margin instead
instr_max_height = trough.wells()[0].top().point.z + 30
height2 = safe_height(
trough.wells()[0].top(), trough2.wells()[0].top(),
deck, round(instr_max_height, 2), 7.0, 15.0)
assert height2 ==\
round(trough.wells()[0].top().point.z, 2) + 15.0
# it fails if the highest deck height is less than 1 mm below
# the max instr achievable height
instr_max_height = trough.wells()[0].top().point.z
with pytest.raises(Exception):
safe_height(
trough.wells()[0].top(), trough2.wells()[0].top(),
deck, round(instr_max_height, 2), 7.0, 15.0)
def test_direct_cp():
deck = Deck()
trough = labware.load(trough_name, deck.position_for(1))
lw1 = labware.load(labware_name, deck.position_for(2))
# when moving from no origin location to a centered labware we should
# start in default cp
from_nothing = plan_moves(Location(Point(50, 50, 50), None),
trough.wells()[0].top(), deck)
check_arc_basic(from_nothing, Location(Point(50, 50, 50), None),
trough.wells()[0].top())
assert from_nothing[0][1] is None
assert from_nothing[1][1] == CriticalPoint.XY_CENTER
assert from_nothing[2][1] == CriticalPoint.XY_CENTER
# when moving from an origin with a centered labware to a dest with a
# centered labware we should stay in centered the entire time, whether
# arc
from_centered_arc = plan_moves(trough.wells()[0].top(),
trough.wells()[1].top(), deck)
check_arc_basic(from_centered_arc,
trough.wells()[0].top(),
trough.wells()[1].top())
assert from_centered_arc[0][1] == CriticalPoint.XY_CENTER
assert from_centered_arc[1][1] == CriticalPoint.XY_CENTER
assert from_centered_arc[2][1] == CriticalPoint.XY_CENTER
# or direct
from_centered_direct = plan_moves(trough.wells()[0].top(),
trough.wells()[1].bottom(), deck)
assert from_centered_direct[0][1] == CriticalPoint.XY_CENTER
# when moving from centered to normal, only the first move should be
# centered
to_normal = plan_moves(trough.wells()[0].top(), lw1.wells()[0].top(), deck)
check_arc_basic(to_normal, trough.wells()[0].top(), lw1.wells()[0].top())
assert to_normal[0][1] == CriticalPoint.XY_CENTER
assert to_normal[1][1] is None
assert to_normal[2][1] is None
def test_add_index_file(labware_name, index_file_dir):
deck = Deck()
parent = deck.position_for(1)
definition = labware.get_labware_definition(labware_name)
lw = labware.Labware(definition, parent)
labware_hash = labware._hash_labware_def(lw._definition)
labware._add_to_index_offset_file(lw, labware_hash)
lw_uri = labware.uri_from_definition(definition)
str_parent = labware._get_parent_identifier(lw.parent)
slot = '1'
if str_parent:
mod_dict = {str_parent: f'{slot}-{str_parent}'}
else:
mod_dict = {}
blob = {
"id": f'{labware_hash}',
"slot": f'{labware_hash}{str_parent}',
"module": mod_dict
}
lw_path = index_file_dir / 'index.json'
info = labware._read_file(lw_path)
assert info[lw_uri] == blob
def test_add_index_file(labware_name, labware_offset_tempdir):
deck = Deck()
parent = deck.position_for(1)
definition = labware.get_labware_definition(labware_name)
lw = labware.Labware(definition, parent)
labware_hash = helpers.hash_labware_def(definition)
labware.save_calibration(lw, Point(0, 0, 0))
lw_uri = helpers.uri_from_definition(definition)
str_parent = labware._get_parent_identifier(lw)
slot = '1'
if str_parent:
mod_dict = {str_parent: f'{slot}-{str_parent}'}
else:
mod_dict = {}
full_id = f'{labware_hash}{str_parent}'
blob = {
"uri": f'{lw_uri}',
"slot": full_id,
"module": mod_dict
}
lw_path = labware_offset_tempdir / 'index.json'
info = file_operators.read_cal_file(lw_path)
assert info['data'][full_id] == blob
def test_no_labware_loc():
labware_def = labware.get_labware_definition(labware_name)
deck = Deck()
lw1 = labware.load(labware_name, deck.position_for(1))
lw2 = labware.load(labware_name, deck.position_for(2))
# Various flavors of locations without labware should work
no_lw = lw1.wells()[0].top()._replace(labware=None)
no_from = plan_moves(no_lw, lw2.wells()[0].bottom(), deck, 7.0, 15.0)
check_arc_basic(no_from, no_lw, lw2.wells()[0].bottom())
assert no_from[0][0].z == deck.highest_z + 15.0
no_to = plan_moves(lw1.wells()[0].bottom(), no_lw, deck, 7.0, 15.0)
check_arc_basic(no_to, lw1.wells()[0].bottom(), no_lw)
assert no_from[0][0].z == deck.highest_z + 15.0
no_well = lw1.wells()[0].top()._replace(labware=lw1)
no_from_well = plan_moves(no_well, lw1.wells()[1].top(), deck, 7.0, 15.0)
check_arc_basic(no_from_well, no_well, lw1.wells()[1].top())
assert no_from_well[0][0].z\
== labware_def['dimensions']['zDimension'] + 7.0
no_to_well = plan_moves(lw1.wells()[1].top(), no_well, deck, 7.0, 15.0)
check_arc_basic(no_to_well, lw1.wells()[1].top(), no_well)
assert no_to_well[0][0].z\
== labware_def['dimensions']['zDimension'] + 7.0
def test_basic_arc():
deck = Deck()
lw1 = labware.load(labware_name, deck.position_for(1))
lw2 = labware.load(labware_name, deck.position_for(2))
deck[1] = lw1
deck[2] = lw2
# same-labware moves should use the smaller safe z
same_lw = plan_moves(lw1.wells()[0].top(),
lw1.wells()[8].bottom(),
deck,
P300M_GEN2_MAX_HEIGHT,
7.0, 15.0)
check_arc_basic(same_lw, lw1.wells()[0].top(), lw1.wells()[8].bottom())
assert same_lw[0][0].z == lw1.wells()[0].top().point.z + 7.0
# different-labware moves, or moves with no labware attached,
# should use the larger safe z and the global z
different_lw = plan_moves(lw1.wells()[0].top(),
lw2.wells()[0].bottom(),
deck,
P300M_GEN2_MAX_HEIGHT,
7.0, 15.0)
check_arc_basic(different_lw,
lw1.wells()[0].top(), lw2.wells()[0].bottom())
assert different_lw[0][0].z == deck.highest_z + 15.0
def test_arc_lower_minimum_z_height():
deck = Deck()
lw1 = labware.load(labware_name, deck.position_for(1))
tall_z = 100
minimum_z_height = 42
old_top = lw1.wells()[0].top()
tall_point = old_top.point._replace(z=tall_z)
tall_top = old_top._replace(point=tall_point)
to_tall = plan_moves(lw1.wells()[2].top(),
tall_top,
deck,
7.0,
15.0,
False,
minimum_z_height=minimum_z_height)
check_arc_basic(to_tall, lw1.wells()[2].top(), tall_top)
assert to_tall[0][0].z == tall_z
from_tall = plan_moves(tall_top,
lw1.wells()[3].top(),
deck,
7.0,
15.0,
minimum_z_height=minimum_z_height)
check_arc_basic(from_tall, tall_top, lw1.wells()[3].top())
assert from_tall[0][0].z == tall_z
no_well = tall_top._replace(labware=lw1)
from_tall_lw = plan_moves(no_well,
lw1.wells()[4].bottom(), deck, 7.0, 15.0)
check_arc_basic(from_tall_lw, no_well, lw1.wells()[4].bottom())
def test_direct_movs():
deck = Deck()
lw1 = labware.load(labware_name, deck.position_for(1))
same_place = plan_moves(lw1.wells()[0].top(), lw1.wells()[0].top(), deck)
assert same_place == [(lw1.wells()[0].top().point, None)]
same_well = plan_moves(lw1.wells()[0].top(), lw1.wells()[0].bottom(), deck)
assert same_well == [(lw1.wells()[0].bottom().point, None)]
def test_direct_minimum_z_height():
deck = Deck()
lw1 = labware.load(labware_name, deck.position_for(1))
from_loc = lw1.wells()[0].bottom().move(Point(x=-2))
to_loc = lw1.wells()[0].bottom().move(Point(x=2))
zmo = 150
# This would normally be a direct move since it’s inside the same well,
# but we want to check that we override it into an arc
moves = plan_moves(from_loc, to_loc, deck, minimum_z_height=zmo)
assert len(moves) == 3
assert moves[0][0].z == zmo # equals zmo b/c 150 is max of all safe z's
check_arc_basic(moves, from_loc, to_loc)
def test_direct_movs():
deck = Deck()
lw1 = labware.load(labware_name, deck.position_for(1))
same_place = plan_moves(
lw1.wells()[0].top(), lw1.wells()[0].top(), deck,
instr_max_height=P300M_GEN2_MAX_HEIGHT)
assert same_place == [(lw1.wells()[0].top().point, None)]
same_well = plan_moves(
lw1.wells()[0].top(), lw1.wells()[0].bottom(), deck,
instr_max_height=P300M_GEN2_MAX_HEIGHT)
assert same_well == [(lw1.wells()[0].bottom().point, None)]
def set_up_index_file_temporary_directory(server_temp_directory):
delete.clear_calibrations()
deck = Deck()
labware_list = [
'nest_96_wellplate_2ml_deep', 'corning_384_wellplate_112ul_flat',
'geb_96_tiprack_1000ul', 'nest_12_reservoir_15ml',
'opentrons_96_tiprack_10ul'
]
for idx, name in enumerate(labware_list):
parent = deck.position_for(idx + 1)
definition = labware.get_labware_definition(name)
lw = labware.Labware(definition, parent)
labware.save_calibration(lw, Point(0, 0, 0))
def set_up_index_file(labware_offset_tempdir):
deck = Deck()
labware_list = [
'nest_96_wellplate_2ml_deep',
'corning_384_wellplate_112ul_flat',
'geb_96_tiprack_1000ul',
'nest_12_reservoir_15ml']
for idx, name in enumerate(labware_list):
parent = deck.position_for(idx+1)
definition = labware.get_labware_definition(name)
lw = labware.Labware(definition, parent)
labware.save_calibration(lw, Point(0, 0, 0))
return labware_list
def test_force_direct():
deck = Deck()
lw1 = labware.load(labware_name, deck.position_for(1))
lw2 = labware.load(labware_name, deck.position_for(2))
# same-labware moves should move direct
same_lw = plan_moves(lw1.wells()[0].top(),
lw1.wells()[8].bottom(),
deck,
P300M_GEN2_MAX_HEIGHT,
7.0, 15.0, force_direct=True)
assert same_lw == [(lw1.wells()[8].bottom().point, None)]
# different-labware moves should move direct
different_lw = plan_moves(lw1.wells()[0].top(),
lw2.wells()[0].bottom(),
deck,
P300M_GEN2_MAX_HEIGHT,
7.0, 15.0, force_direct=True)
assert different_lw == [(lw2.wells()[0].bottom().point, None)]
def test_slot_collisions():
d = Deck()
mod_slot = '7'
mod = labware.load_module('thermocycler', d.position_for(mod_slot))
d[mod_slot] = mod
with pytest.raises(ValueError):
d['7'] = 'not this time boyo'
with pytest.raises(ValueError):
d['8'] = 'nor this time boyo'
with pytest.raises(ValueError):
d['10'] = 'or even this time boyo'
with pytest.raises(ValueError):
d['11'] = 'def not this time though'
lw_slot = '4'
lw = labware.load(labware_name, d.position_for(lw_slot))
d[lw_slot] = lw
assert lw_slot in d
def test_first_parent():
deck = Deck()
trough = labware.load(trough_name, deck.position_for(1))
assert first_parent(trough) == '1'
assert first_parent(trough['A2']) == '1'
assert first_parent(None) is None
assert first_parent('6') == '6'
mod = module_geometry.load_module(
module_geometry.TemperatureModuleModel.TEMPERATURE_V2,
deck.position_for('6'), MAX_SUPPORTED_VERSION)
mod_trough = mod.add_labware(labware.load(trough_name, mod.location))
assert first_parent(mod_trough['A5']) == '6'
assert first_parent(mod_trough) == '6'
assert first_parent(mod) == '6'
mod_trough._parent = mod_trough
with pytest.raises(RuntimeError):
# make sure we catch cycles
first_parent(mod_trough)
def test_labware_in_next_slow():
deck = Deck()
trough = labware.load(trough_name, deck.position_for(4))
trough2 = labware.load(trough_name, deck.position_for(1))
trough3 = labware.load(trough_name, deck.position_for(3))
deck[4] = trough
deck[1] = trough2
deck[3] = trough3
assert deck.right_of('3') is None
assert deck.left_of('2') is trough2
assert deck.right_of('2') is trough3
assert deck.right_of('9') is None
def test_slot_names():
slots_by_int = list(range(1, 13))
slots_by_str = [str(idx) for idx in slots_by_int]
for method in (slots_by_int, slots_by_str):
d = Deck()
for idx, slot in enumerate(method):
lw = labware.load(labware_name, d.position_for(slot))
assert slot in d
d[slot] = lw
with pytest.raises(ValueError):
d[slot] = 'not this time boyo'
del d[slot]
assert slot in d
assert d[slot] is None
mod = labware.load_module('tempdeck', d.position_for(slot))
d[slot] = mod
assert mod == d[slot]
assert 'hasasdaia' not in d
with pytest.raises(ValueError):
d['ahgoasia'] = 'nope'
def test_no_labware_loc(labware_offset_tempdir):
labware_def = labware.get_labware_definition(labware_name)
deck = Deck()
lw1 = labware.load(labware_name, deck.position_for(1))
lw2 = labware.load(labware_name, deck.position_for(2))
deck[1] = lw1
deck[2] = lw2
# Various flavors of locations without labware should work
no_lw = lw1.wells()[0].top()._replace(labware=None)
no_from = plan_moves(no_lw,
lw2.wells()[0].bottom(), deck, P300M_GEN2_MAX_HEIGHT,
7.0, 15.0)
check_arc_basic(no_from, no_lw, lw2.wells()[0].bottom())
assert no_from[0][0].z == deck.highest_z + 15.0
no_to = plan_moves(lw1.wells()[0].bottom(), no_lw, deck,
P300M_GEN2_MAX_HEIGHT, 7.0, 15.0)
check_arc_basic(no_to, lw1.wells()[0].bottom(), no_lw)
assert no_from[0][0].z == deck.highest_z + 15.0
no_well = lw1.wells()[0].top()._replace(labware=lw1)
no_from_well = plan_moves(no_well,
lw1.wells()[1].top(), deck,
P300M_GEN2_MAX_HEIGHT, 7.0, 15.0)
check_arc_basic(no_from_well, no_well, lw1.wells()[1].top())
no_from_well_height = no_from_well[0][0].z
lw_height_expected = labware_def['dimensions']['zDimension'] + 7
assert no_from_well_height == lw_height_expected
no_to_well = plan_moves(lw1.wells()[1].top(), no_well, deck,
P300M_GEN2_MAX_HEIGHT, 7.0, 15.0)
check_arc_basic(no_to_well, lw1.wells()[1].top(), no_well)
no_to_well_height = no_to_well[0][0].z
assert no_to_well_height == lw_height_expected
def test_highest_z():
deck = Deck()
fixed_trash = deck.get_fixed_trash()
assert deck.highest_z == fixed_trash.highest_z
tall_lw = labware.load(tall_lw_name, deck.position_for(1))
deck[1] = tall_lw
assert deck.highest_z == pytest.approx(tall_lw.wells()[0].top().point.z)
del deck[1]
assert deck.highest_z == fixed_trash.highest_z
mod = module_geometry.load_module(
module_geometry.TemperatureModuleModel.TEMPERATURE_V1,
deck.position_for(8))
deck[8] = mod
assert deck.highest_z == mod.highest_z
lw = labware.load(labware_name, mod.location)
mod.add_labware(lw)
deck.recalculate_high_z()
assert deck.highest_z == mod.highest_z
def test_highest_z():
deck = Deck()
assert deck.highest_z == 0
lw = labware.load(labware_name, deck.position_for(1))
deck[1] = lw
assert deck.highest_z == pytest.approx(lw.wells()[0].top().point.z)
del deck[1]
assert deck.highest_z == 0
mod = labware.load_module('tempdeck', deck.position_for(8))
deck[8] = mod
assert deck.highest_z == mod.highest_z
lw = labware.load(labware_name, mod.location)
mod.add_labware(lw)
deck.recalculate_high_z()
assert deck.highest_z == mod.highest_z
def test_build_edges():
lw_def = get_labware_definition('corning_96_wellplate_360ul_flat')
test_lw = Labware(lw_def, Location(Point(0, 0, 0), None))
off = Point(0, 0, 1.0)
deck = Deck()
old_correct_edges = [
test_lw['A1']._from_center_cartesian(x=1.0, y=0, z=1) + off,
test_lw['A1']._from_center_cartesian(x=-1.0, y=0, z=1) + off,
test_lw['A1']._from_center_cartesian(x=0, y=1.0, z=1) + off,
test_lw['A1']._from_center_cartesian(x=0, y=-1.0, z=1) + off,
]
res = build_edges(test_lw['A1'], 1.0, APIVersion(2, 2), Mount.RIGHT, deck)
assert res == old_correct_edges
new_correct_edges = [
test_lw['A1']._from_center_cartesian(x=1.0, y=0, z=1) + off,
test_lw['A1']._from_center_cartesian(x=-1.0, y=0, z=1) + off,
test_lw['A1']._from_center_cartesian(x=0, y=0, z=1) + off,
test_lw['A1']._from_center_cartesian(x=0, y=1.0, z=1) + off,
test_lw['A1']._from_center_cartesian(x=0, y=-1.0, z=1) + off,
]
res2 = build_edges(test_lw['A1'], 1.0, APIVersion(2, 4), Mount.RIGHT, deck)
assert res2 == new_correct_edges
def test_gen2_module_transforms():
deck = Deck()
tmod = module_geometry.load_module(
module_geometry.TemperatureModuleModel.TEMPERATURE_V2,
deck.position_for('1'), MAX_SUPPORTED_VERSION)
assert tmod.labware_offset == Point(-1.45, -0.15, 80.09)
tmod2 = module_geometry.load_module(
module_geometry.TemperatureModuleModel.TEMPERATURE_V2,
deck.position_for('3'), MAX_SUPPORTED_VERSION)
assert tmod2.labware_offset == Point(1.15, -0.15, 80.09)
mmod = module_geometry.load_module(
module_geometry.MagneticModuleModel.MAGNETIC_V2,
deck.position_for('1'), MAX_SUPPORTED_VERSION)
assert mmod.labware_offset == Point(-1.175, -0.125, 82.25)
mmod2 = module_geometry.load_module(
module_geometry.MagneticModuleModel.MAGNETIC_V2,
deck.position_for('3'), MAX_SUPPORTED_VERSION)
assert mmod2.labware_offset == Point(1.425, -0.125, 82.25)
def test_should_dodge():
deck = Deck()
# with no tc loaded, doesn't matter what the positions are
assert not should_dodge_thermocycler(
deck, deck.position_for(4), deck.position_for(9))
deck[7] = module_geometry.load_module(
module_geometry.ThermocyclerModuleModel.THERMOCYCLER_V1,
deck.position_for(7))
# with a tc loaded, some positions should require dodging
assert should_dodge_thermocycler(
deck, deck.position_for(12), deck.position_for(1))
# but ones that weren't explicitly marked shouldn't
assert not should_dodge_thermocycler(
deck, deck.position_for(1), deck.position_for(2))
# including a situation where we might have some messed up locations
# with no parent
assert not should_dodge_thermocycler(
deck,
deck.position_for(1)._replace(labware=None),
deck.position_for(12)
)
def test_get_non_fixture_slots():
deck = Deck()
trough = labware.load(trough_name, deck.position_for(4))
deck[4] = trough
assert deck.get_non_fixture_slots() == [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]
