def test_tip_tracking_init():
labware_name = 'opentrons_96_tiprack_300ul'
labware_def = labware.get_labware_definition(labware_name)
tiprack = labware.Labware(labware_def,
Location(Point(0, 0, 0), 'Test Slot'))
assert tiprack.is_tiprack
for well in tiprack.wells():
assert well.has_tip
labware_name = 'corning_96_wellplate_360ul_flat'
labware_def = labware.get_labware_definition(labware_name)
lw = labware.Labware(labware_def, Location(Point(0, 0, 0), 'Test Slot'))
assert not lw.is_tiprack
for well in lw.wells():
assert not well.has_tip
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_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 load_new_labware(container_name):
""" Load a labware in the new schema into a placeable, by name
:raises KeyError: If the labware name is not found
"""
defn = new_labware.get_labware_definition(load_name=container_name)
return load_new_labware_def(defn)
def _determine_required_labware(self) -> typing.Dict[UUID, LabwareInfo]:
"""
A function that inserts tiprack information into two dataclasses
:py:class:`.LabwareInfo` and :py:class:`.LabwareDefinition` based
on the current pipettes attached.
"""
lw: typing.Dict[UUID, LabwareInfo] = {}
_prev_lw_uuid: typing.Optional[UUID] = None
for mount, pip_info in self._pip_info_by_mount.items():
load_name: str = self._load_name_for_mount(mount)
prev_lw = lw.get(_prev_lw_uuid, None) if _prev_lw_uuid else None
if _prev_lw_uuid and prev_lw and prev_lw.loadName == load_name:
# pipette uses same tiprack as previous, use existing
lw[_prev_lw_uuid].forMounts.append(mount)
self._pip_info_by_mount[mount].tiprack_id = _prev_lw_uuid
else:
lw_def = labware.get_labware_definition(load_name)
new_uuid: UUID = uuid4()
_prev_lw_uuid = new_uuid
slot = self._get_tip_rack_slot_for_mount(mount)
lw[new_uuid] = LabwareInfo(
alternatives=self._alt_load_names_for_mount(mount),
forMounts=[mount],
loadName=load_name,
slot=slot,
namespace=lw_def['namespace'],
version=lw_def['version'],
id=new_uuid,
definition=lw_def)
self._pip_info_by_mount[mount].tiprack_id = new_uuid
return lw
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_tiprack_list():
labware_name = 'opentrons_96_tiprack_300ul'
labware_def = labware.get_labware_definition(labware_name)
tiprack = labware.Labware(labware_def,
Location(Point(0, 0, 0), 'Test Slot'))
tiprack_2 = labware.Labware(labware_def,
Location(Point(0, 0, 0), 'Test Slot'))
assert labware.select_tiprack_from_list(
[tiprack], 1) == (tiprack, tiprack['A1'])
assert labware.select_tiprack_from_list(
[tiprack], 1, tiprack.wells()[1]) == (tiprack, tiprack['B1'])
tiprack['C1'].has_tip = False
assert labware.select_tiprack_from_list(
[tiprack], 1, tiprack.wells()[2]) == (tiprack, tiprack['D1'])
tiprack['H12'].has_tip = False
tiprack_2['A1'].has_tip = False
assert labware.select_tiprack_from_list(
[tiprack, tiprack_2], 1, tiprack.wells()[95]) == (
tiprack_2, tiprack_2['B1'])
with pytest.raises(labware.OutOfTipsError):
labware.select_tiprack_from_list(
[tiprack], 1, tiprack.wells()[95])
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, Mount.RIGHT, deck, version=APIVersion(2, 2))
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, Mount.RIGHT, deck, version=APIVersion(2, 4))
assert res2 == new_correct_edges
def test_select_next_tip():
labware_name = 'opentrons_96_tiprack_300ul'
labware_def = labware.get_labware_definition(labware_name)
tiprack = labware.Labware(labware_def,
Location(Point(0, 0, 0), 'Test Slot'))
well_list = tiprack.wells()
next_one = tiprack.next_tip()
assert next_one == well_list[0]
next_five = tiprack.next_tip(5)
assert next_five == well_list[0]
next_eight = tiprack.next_tip(8)
assert next_eight == well_list[0]
next_nine = tiprack.next_tip(9)
assert next_nine is None
# A1 tip only has been used
tiprack.use_tips(well_list[0])
next_one = tiprack.next_tip()
assert next_one == well_list[1]
next_five = tiprack.next_tip(5)
assert next_five == well_list[1]
next_eight = tiprack.next_tip(8)
assert next_eight == well_list[8]
# 2nd column has also been used
tiprack.use_tips(well_list[8], num_channels=8)
next_one = tiprack.next_tip()
assert next_one == well_list[1]
next_five = tiprack.next_tip(5)
assert next_five == well_list[1]
next_eight = tiprack.next_tip(8)
assert next_eight == well_list[16]
# Bottom 4 tips of 1rd column are also used
tiprack.use_tips(well_list[4], num_channels=4)
next_one = tiprack.next_tip()
assert next_one == well_list[1]
next_three = tiprack.next_tip(3)
assert next_three == well_list[1]
next_five = tiprack.next_tip(5)
assert next_five == well_list[16]
next_eight = tiprack.next_tip(8)
assert next_eight == well_list[16]
# you can reuse tips infinitely on api level 2.2
tiprack.use_tips(well_list[0])
tiprack.use_tips(well_list[0])
# you can't on api level 2.1 or previous
early_tr = labware.Labware(labware_def,
Location(Point(0, 0, 0), 'Test Slot'),
api_level=APIVersion(2, 1))
early_tr.use_tips(well_list[0])
with pytest.raises(AssertionError):
early_tr.use_tips(well_list[0])
def test_uris():
details = ('opentrons', 'opentrons_96_tiprack_300ul', '1')
uri = 'opentrons/opentrons_96_tiprack_300ul/1'
assert labware.uri_from_details(*details) == uri
defn = labware.get_labware_definition(details[1], details[0], details[2])
assert labware.uri_from_definition(defn) == uri
lw = labware.Labware(defn, Location(Point(0, 0, 0), 'Test Slot'))
assert lw.uri == uri
def mock_user_flow(mock_hw, request):
has_calibration_block = request.param
mount = next(k for k, v in mock_hw._attached_instruments.items() if v)
pip_model = mock_hw._attached_instruments[mount].model
tip_rack = get_labware_definition(pipette_map[pip_model], 'opentrons', '1')
m = TipCalibrationUserFlow(hardware=mock_hw,
mount=mount,
has_calibration_block=has_calibration_block,
tip_rack=tip_rack)
yield m
def load_new_labware(container_name, version=None):
""" Load a labware in the new schema into a placeable, by name and version
:param container_name: The load name of the container
:param version: the version to load.
:raises KeyError: If the labware name is not found
"""
defn = new_labware.get_labware_definition(load_name=container_name,
version=version)
return load_new_labware_def(defn)
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_well_parent():
labware_name = 'corning_96_wellplate_360ul_flat'
labware_def = labware.get_labware_definition(labware_name)
lw = labware.Labware(labware_def, Location(Point(0, 0, 0), 'Test Slot'))
parent = Location(Point(7, 8, 9), lw)
well_name = 'circular_well_json'
has_tip = True
well = labware.Well(test_data[well_name], parent, well_name, has_tip)
assert well.parent is lw
assert well.top().labware is well
assert well.top().labware.parent is lw
assert well.bottom().labware is well
assert well.bottom().labware.parent is lw
assert well.center().labware is well
assert well.center().labware.parent is lw
def test_get_parent_identifier():
labware_name = 'corning_96_wellplate_360ul_flat'
labware_def = labware.get_labware_definition(labware_name)
lw = labware.Labware(labware_def, Location(Point(0, 0, 0), 'Test Slot'))
# slots have no parent identifier
assert labware._get_parent_identifier(lw) == ''
# modules do
mmg = ModuleGeometry('my magdeck',
MagneticModuleModel.MAGNETIC_V1,
ModuleType.MAGNETIC,
Point(0, 0, 0), 10, 10, Location(Point(1, 2, 3), '3'),
APIVersion(2, 4))
lw = labware.Labware(labware_def, mmg.location)
assert labware._get_parent_identifier(lw)\
== MagneticModuleModel.MAGNETIC_V1.value
def test_select_next_tip():
labware_name = 'opentrons_96_tiprack_300ul'
labware_def = labware.get_labware_definition(labware_name)
tiprack = labware.Labware(labware_def,
Location(Point(0, 0, 0), 'Test Slot'))
well_list = tiprack.wells()
next_one = tiprack.next_tip()
assert next_one == well_list[0]
next_five = tiprack.next_tip(5)
assert next_five == well_list[0]
next_eight = tiprack.next_tip(8)
assert next_eight == well_list[0]
next_nine = tiprack.next_tip(9)
assert next_nine is None
# A1 tip only has been used
tiprack.use_tips(well_list[0])
next_one = tiprack.next_tip()
assert next_one == well_list[1]
next_five = tiprack.next_tip(5)
assert next_five == well_list[1]
next_eight = tiprack.next_tip(8)
assert next_eight == well_list[8]
# 2nd column has also been used
tiprack.use_tips(well_list[8], num_channels=8)
next_one = tiprack.next_tip()
assert next_one == well_list[1]
next_five = tiprack.next_tip(5)
assert next_five == well_list[1]
next_eight = tiprack.next_tip(8)
assert next_eight == well_list[16]
# Bottom 4 tips of 1rd column are also used
tiprack.use_tips(well_list[4], num_channels=4)
next_one = tiprack.next_tip()
assert next_one == well_list[1]
next_three = tiprack.next_tip(3)
assert next_three == well_list[1]
next_five = tiprack.next_tip(5)
assert next_five == well_list[16]
next_eight = tiprack.next_tip(8)
assert next_eight == well_list[16]
def test_module_load_labware(module_name):
labware_name = 'corning_96_wellplate_360ul_flat'
labware_def = labware.get_labware_definition(labware_name)
model = module_geometry.resolve_module_model(module_name)
mod = module_geometry.load_module(model, Location(Point(0, 0, 0), 'test'))
old_z = mod.highest_z
lw = labware.load_from_definition(labware_def, mod.location)
mod.add_labware(lw)
assert mod.labware == lw
assert mod.highest_z ==\
(mod.location.point.z
+ labware_def['dimensions']['zDimension']
+ mod._over_labware)
with pytest.raises(AssertionError):
mod.add_labware(lw)
mod.reset_labware()
assert mod.labware is None
assert mod.highest_z == old_z
def test_previous_tip():
labware_name = 'opentrons_96_tiprack_300ul'
labware_def = labware.get_labware_definition(labware_name)
tiprack = labware.Labware(labware_def,
Location(Point(0, 0, 0), 'Test Slot'))
# If all wells are used, we can't get a previous tip
assert tiprack.previous_tip() is None
# If one well is empty, wherever it is, we can get a slot
tiprack.wells()[5].has_tip = False
assert tiprack.previous_tip() is tiprack.wells()[5]
# But not if we ask for more slots than are available
assert tiprack.previous_tip(2) is None
tiprack.wells()[7].has_tip = False
# And those available wells have to be contiguous
assert tiprack.previous_tip(2) is None
# But if they are, we're good
tiprack.wells()[6].has_tip = False
assert tiprack.previous_tip(3) is tiprack.wells()[5]
def test_back_compat():
labware_name = 'corning_96_wellplate_360ul_flat'
labware_def = labware.get_labware_definition(labware_name)
lw = labware.Labware(labware_def, Location(Point(0, 0, 0), 'Test Slot'))
# Note that this test uses the display name of wells to test for equality,
# because dimensional parameters could be subject to modification through
# calibration, whereas here we are testing for "identity" in a way that is
# related to the combination of well name, labware name, and slot name
well_a1_name = repr(lw.wells_by_name()['A1'])
well_b2_name = repr(lw.wells_by_name()['B2'])
well_c3_name = repr(lw.wells_by_name()['C3'])
w2 = lw.well(0)
assert repr(w2) == well_a1_name
w3 = lw.well('A1')
assert repr(w3) == well_a1_name
w4 = lw.wells('B2')
assert repr(w4[0]) == well_b2_name
w5 = lw.wells(9, 21, 25, 27)
assert len(w5) == 4
assert repr(w5[0]) == well_b2_name
w6 = lw.wells('A1', 'B2', 'C3')
assert all([
repr(well[0]) == well[1]
for well in zip(w6, [well_a1_name, well_b2_name, well_c3_name])
])
w7 = lw.rows('A')
assert len(w7) == 1
assert repr(w7[0][0]) == well_a1_name
w8 = lw.rows('A', 'C')
assert len(w8) == 2
assert repr(w8[0][0]) == well_a1_name
assert repr(w8[1][2]) == well_c3_name
w11 = lw.columns('2', '3', '6')
assert len(w11) == 3
assert repr(w11[1][2]) == well_c3_name
def test_module_load_labware():
module_names = ['tempdeck', 'magdeck']
labware_name = 'corning_96_wellplate_360ul_flat'
labware_def = labware.get_labware_definition(labware_name)
for name in module_names:
mod = labware.load_module(name, Location(Point(0, 0, 0), 'test'))
old_z = mod.highest_z
lw = labware.load_from_definition(labware_def, mod.location)
mod.add_labware(lw)
assert mod.labware == lw
assert mod.highest_z ==\
(mod.location.point.z
+ labware_def['dimensions']['zDimension']
+ mod._over_labware)
with pytest.raises(AssertionError):
mod.add_labware(lw)
mod.reset_labware()
assert mod.labware is None
assert mod.highest_z == old_z
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 _determine_required_labware(self) -> typing.Dict[UUID, LabwareInfo]:
"""
A function that inserts tiprack information into two dataclasses
:py:class:`.LabwareInfo` and :py:class:`.LabwareDefinition` based
on the current pipettes attached.
"""
lw: typing.Dict[UUID, LabwareInfo] = {}
_uuid: typing.Optional[UUID] = None
for pipette_id in self._relate_mount.keys():
mount = self._get_mount(pipette_id)
pip_vol = self.get_pipette(mount)['max_volume']
_lookup = LOOKUP_LABWARE[str(pip_vol)]
load_name: str = _lookup.load_name
if_labware = None
if _uuid:
if_labware = lw.get(_uuid)
if _uuid and if_labware and if_labware.loadName == load_name:
lw[_uuid].forPipettes.append(pipette_id)
self._relate_mount[pipette_id]['tiprack_id'] = _uuid
else:
lw_def = labware.get_labware_definition(load_name)
new_uuid: UUID = uuid4()
_uuid = new_uuid
slot = self._available_slot_options()
lw[new_uuid] = LabwareInfo(
alternatives=list(_lookup.alternatives),
forPipettes=[pipette_id],
loadName=load_name,
slot=slot,
namespace=lw_def['namespace'],
version=lw_def['version'],
id=new_uuid,
definition=lw_def)
self._relate_mount[pipette_id]['tiprack_id'] = new_uuid
return lw
def test_return_tips():
labware_name = 'opentrons_96_tiprack_300ul'
labware_def = labware.get_labware_definition(labware_name)
tiprack = labware.Labware(labware_def,
Location(Point(0, 0, 0), 'Test Slot'))
# If all wells are used, we get an error if we try to return
with pytest.raises(AssertionError):
tiprack.return_tips(tiprack.wells()[0])
# If we have space where we specify, everything is OK
tiprack.wells()[0].has_tip = False
tiprack.return_tips(tiprack.wells()[0])
assert tiprack.wells()[0].has_tip
# We have to have enough space
tiprack.wells()[0].has_tip = False
with pytest.raises(AssertionError):
tiprack.return_tips(tiprack.wells()[0], 2)
# But we can drop stuff off the end of a column
tiprack.wells()[7].has_tip = False
tiprack.wells()[8].has_tip = False
tiprack.return_tips(tiprack.wells()[7], 2)
assert tiprack.wells()[7].has_tip
# But we won't wrap around
assert not tiprack.wells()[8].has_tip
def test_use_tips():
labware_name = 'opentrons_96_tiprack_300ul'
labware_def = labware.get_labware_definition(labware_name)
tiprack = labware.Labware(labware_def,
Location(Point(0, 0, 0), 'Test Slot'))
well_list = tiprack.wells()
# Test only using one tip
tiprack.use_tips(well_list[0])
assert not well_list[0].has_tip
for well in well_list[1:]:
assert well.has_tip
# Test using a whole column
tiprack.use_tips(well_list[8], num_channels=8)
for well in well_list[8:16]:
assert not well.has_tip
assert well_list[7].has_tip
assert well_list[16].has_tip
# Test using a partial column from the top
tiprack.use_tips(well_list[16], num_channels=4)
for well in well_list[16:20]:
assert not well.has_tip
for well in well_list[20:24]:
assert well.has_tip
# Test using a partial column where the number of tips that get picked up
# is less than the number of channels (e.g.: an 8-channel pipette picking
# up 4 tips from the bottom half of a column)
tiprack.use_tips(well_list[28], num_channels=4)
for well in well_list[24:28]:
assert well.has_tip
for well in well_list[28:32]:
assert not well.has_tip
for well in well_list[32:]:
assert well.has_tip
