def test_purify(self, mock_sleep, mock_serial,
mock_writeAndWait, mock_pickUpNextTip,
mock_mixByScript, mock_transferLiquid, mock_dumpTipToWaste, mock_uptakeLiquid,
mock_moveAxisDelta):
p = ponec.protocol(self.ber, self.settings)
p.purify()
p2 = ponec.protocol(self.ber, self.settings2)
p2.purify()
def test_getAlreadyWaitedTime(self):
p = ponec.protocol(self.ber, self.settings)
p.timestamp = time.time()
time.sleep(0.05)
result = p.getAlreadyWaitedTime()
self.assertTrue(result > 0.05)
self.assertTrue(result < 0.07)
def test_purify__one_stage__pipette_speed(self,
mock_setSpeedPipette, mock_sleep, mock_serial,
mock_writeAndWait, mock_pickUpNextTip,
mock_mixByScript, mock_transferLiquid, mock_dumpTipToWaste, mock_uptakeLiquid,
mock_moveAxisDelta):
p = ponec.protocol(self.ber, self.settings)
p.purify()
# Adding beads
self.assertEqual(mock_setSpeedPipette.mock_calls[0], mock.call(1500.0))
self.assertEqual(mock_setSpeedPipette.mock_calls[1], mock.call(2500.0))
# Removing sup
self.assertEqual(mock_setSpeedPipette.mock_calls[2], mock.call(1500.0))
self.assertEqual(mock_setSpeedPipette.mock_calls[3], mock.call(2500.0))
# Adding ethanol 1st stage
self.assertEqual(mock_setSpeedPipette.mock_calls[4], mock.call(2000.0))
self.assertEqual(mock_setSpeedPipette.mock_calls[5], mock.call(2500.0))
# Removing ethanol 1st stage
self.assertEqual(mock_setSpeedPipette.mock_calls[6], mock.call(2000.0))
self.assertEqual(mock_setSpeedPipette.mock_calls[7], mock.call(2500.0))
# Adding ethanol 2nd stage
self.assertEqual(mock_setSpeedPipette.mock_calls[8], mock.call(2000.0))
self.assertEqual(mock_setSpeedPipette.mock_calls[9], mock.call(2500.0))
# Removing ethanol 2nd stage
self.assertEqual(mock_setSpeedPipette.mock_calls[10], mock.call(2000.0))
self.assertEqual(mock_setSpeedPipette.mock_calls[11], mock.call(2500.0))
# Adding eluent
self.assertEqual(mock_setSpeedPipette.mock_calls[12], mock.call(1800.0))
self.assertEqual(mock_setSpeedPipette.mock_calls[13], mock.call(2500.0))
# Transferring eluate to the results tubes
self.assertEqual(mock_setSpeedPipette.mock_calls[14], mock.call(1800.0))
self.assertEqual(mock_setSpeedPipette.mock_calls[15], mock.call(2500.0))
def test_getDelayBetweenActions(self):
p = ponec.protocol(self.ber, self.settings)
r = p.getDelayBetweenActions(100, 0)
self.assertEqual(r, 100)
r = p.getDelayBetweenActions(100, 1)
self.assertEqual(r, 50)
r = p.getDelayBetweenActions(100, -1)
self.assertEqual(r, 100)
def test_transferLiquidManyTubes(self, mock_transferLiquid, mock_move,
mock_dumpTipToWaste, mock_pickUpNextTip):
p = ponec.protocol(self.ber, self.settings)
p.transferLiquidManyTubes(sources=p.tubes.samples_list,
destinations=p.tubes.result_list,
v_list=self.settings.beads_vol_1st_stage_list)
p.transferLiquidManyTubes(sources=p.tubes.samples_list,
destinations=p.tubes.result_list)
def test_purify_two_stages(self, mock_absrobDNA, mock_transfer, mock_remsup,
mock_etWash, mock_elution):
p2 = ponec.protocol(self.ber, self.settings2)
p2.purify()
mock_transfer.assert_called()
mock_absrobDNA.assert_called()
mock_remsup.assert_called()
mock_etWash.assert_called()
mock_elution.assert_called()
def test_purify__one_stage__pipette_delay(self,
mock_sleep, mock_serial, mock_writeAndWait, mock_pickUpNextTip,
mock_mixByScript, mock_transferLiquid, mock_dumpTipToWaste, mock_uptakeLiquid,
mock_moveAxisDelta):
p = ponec.protocol(self.ber, self.settings)
p.purify()
for call in mock_transferLiquid.mock_calls:
self.assertEqual(call[2]['delay'], 1.0)
def test__init_protocol(self):
"""
Check whether the protocol would even initialize
"""
p = ponec.protocol(self.ber, self.settings)
self.assertEqual(p.robot, self.ber)
self.assertEqual(p.settings, self.settings)
self.assertEqual(p.tubes.samples_list[0].getVolume(), 100)
self.assertEqual(p.default_pipette_speed, 2500.0)
self.assertEqual(p.incubation_time, 0)
def test_incubate(self, mock_mixManySamples):
p = ponec.protocol(self.ber, self.settings)
p.timestamp = time.time()
local_timestamp = time.time()
time_to_wait = 0.05
p.incubation_time = time_to_wait
p.incubate()
time_waited = time.time() - local_timestamp
self.assertTrue(time_waited > time_to_wait)
self.assertTrue(time_waited < time_to_wait+0.2)
def test_transferSamplesToSecondStage(self, mock_pickUpTip, mock_dumpTip,
mock_transferLiquid):
self.assertEqual(self.settings2.V_beads_list,
self.settings2.beads_vol_1st_stage_list)
p2 = ponec.protocol(self.ber, self.settings2)
self.assertEqual(p2.tubes.samples_list[0].getWell(), (1, 0))
p2.transferSamplesToSecondStage()
self.assertEqual(self.settings2.V_beads_list,
self.settings2.beads_vol_2nd_stage_list)
self.assertEqual(p2.tubes.samples_list[0].getWell(), (1, 6))
def test_elution_incubation(self, mock_setSpeedPipette, mock_addEluentToAll,
mock_mixManySamples, mock_pullBeads, mock_transferLiquidManyTubes):
p = ponec.protocol(self.ber, self.settings)
p.timestamp = time.time()
local_timestamp = time.time()
time_to_wait = 0.05
# Temporarily overwriting the setting
p.settings.T_elute = time_to_wait
p.elution()
time_waited = time.time() - local_timestamp
self.assertTrue(time_waited > time_to_wait)
self.assertTrue(time_waited < time_to_wait+0.2)
mock_mixManySamples.is_called()
def test_absorbDNAOntoBeads_incubation(self, mock_addBeads, mock_mixManySamples,
mock_pullBeads):
p = ponec.protocol(self.ber, self.settings)
p.timestamp = time.time()
local_timestamp = time.time()
time_to_wait = 0.05
# Temporarily overwriting the setting
p.settings.T_absorption = time_to_wait
p.absorbDnaOntoBeads()
time_waited = time.time() - local_timestamp
self.assertTrue(time_waited > time_to_wait)
self.assertTrue(time_waited < time_to_wait+0.2)
mock_mixManySamples.is_called()
def test__reinitializeTubesForSecondCleanup(self):
p = ponec.protocol(self.ber, self.settings2)
p.settings.cleanups = 2
p.settings.positions_2nd_stage_tubes = p.settings.positionsToPurify2ndStage()
p.tubes.intermediate_list = p.tubes.initIntermediate()
p.tubes.result_column = 1
p.tubes.result_row = 6
p.tubes.result_list = p.tubes.initResults()
self.assertEqual(p.settings.cleanups, 2)
self.assertEqual(p.tubes.samples_list[0].getWell(), (1,0))
self.assertEqual(p.tubes.intermediate_list[0].getWell(), (1,3))
p._reinitializeTubesForSecondCleanup()
self.assertEqual(p.tubes.samples_list[0].getWell(), (1,6))
self.assertEqual(p.tubes.intermediate_list[0].getWell(), (1,9))
self.assertEqual(p.tubes.result_list[0].getWell(), (0,0))
def test_mixManySamples(self, mock_mix, mock_pickUpNextTip, mock_dumpTipToWaste,
mock_moveAxisDelta, mock_move):
p = ponec.protocol(self.ber, self.settings)
p.mixManySamples()
for call, expected_sample in zip(mock_mix.mock_calls, p.tubes.samples_list):
self.assertEqual(call[1][0], expected_sample)
def test_moveToSafe(self, mock_move):
p = ponec.protocol(self.ber, self.settings)
p.moveToSafe()
mock_move.assert_called_with(z=self.settings.z_safe)
def test_removeSupernatant(self, mock_transferLiquid, mock_move,
mock_dumpTipToWaste, mock_pickUpNextTip):
p = ponec.protocol(self.ber, self.settings)
p.removeSupernatant()