def setUp(self, mock_serial, mock_sleep):
logging.disable(logging.CRITICAL)
self.ber = bl.robot(cartesian_port_name='COM1',
loadcell_port_name='COM2')
self.s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1,
0, 0)
self.beads_5ml = bl.createSample('5mL', 'beads_5ml',
self.ber.samples_rack, 1, 0, 0)
self.eppendorf_mix_script_file_path = 'eppendorf_mix_script.csv'
def test_isLowVolumeUptakeNeeded(self):
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0, 1000)
self.assertEqual(s1.getCloseToBottomVol(), 50)
self.assertEqual(s1.getVolume(), 1000)
self.assertEqual(s1.getExtraImmersionVol(), 200)
low_volume_uptake_needed = s1._isLowVolumeUptakeNeeded(0)
self.assertFalse(low_volume_uptake_needed)
low_volume_uptake_needed = s1._isLowVolumeUptakeNeeded(250)
self.assertFalse(low_volume_uptake_needed)
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0, 200)
low_volume_uptake_needed = s1._isLowVolumeUptakeNeeded(0)
self.assertTrue(low_volume_uptake_needed)
def test_MixScriptSettings(self):
# Creating mock mix script file
line1 = "Height,H_relative_to,Plunger_pos,dx,dy,min_vol_condition,max_vol_condition,delay,comment\n"
line2 = "0,top,down,0,0,0,1700,0.5,Initially lowering the plunger\n"
line3 = "1,bottom,up,0,0,0,250,0.5,mixing in place\n"
with open(self.mix_script_filename, mode='a') as csv_file:
csv_file.write(line1)
csv_file.write(line2)
csv_file.write(line3)
# Making sure the file was in fact created
self.assertTrue(os.path.exists(self.mix_script_filename))
# Making sure the file reads
df = pd.read_csv(self.mix_script_filename)
self.assertEqual(df['Height'][0], 0)
self.assertEqual(df['Height'][1], 1)
self.assertEqual(df['H_relative_to'][0], 'top')
self.assertEqual(df['H_relative_to'][1], 'bottom')
# Creating a sample_name
s1 = bl.createSample(self.sample_type, self.sample_name, self.ber.samples_rack, 1, 0, 0)
# Saving mix script file path
s1.stype.setMixScriptFilePath(self.mix_script_filename)
# Testing whether file name was saved
self.assertTrue(os.path.exists(self.sample_type+'.json'))
self.assertEqual(s1.stype.data['mix_script_file_path'], self.mix_script_filename)
self.assertEqual(s1.stype.getMixScriptFilePath(), self.mix_script_filename)
# Testing whether the dataframe obtained through getMixScript is correct
df = s1.stype.getMixScript()
self.assertEqual(df['Height'][0], 0)
self.assertEqual(df['Height'][1], 1)
self.assertEqual(df['H_relative_to'][0], 'top')
self.assertEqual(df['H_relative_to'][1], 'bottom')
def test_SaveSampleTypeSetting(self):
s1 = bl.createSample(self.sample_type, self.sample_name, self.ber.samples_rack, 1, 0, 0)
s1.stype._setSetting('new_setting_name', 'asdf')
self.assertTrue(os.path.exists(self.sample_type+'.json'))
self.assertEqual(s1.stype.data['new_setting_name'], 'asdf')
self.assertEqual(s1.stype._getSetting('new_setting_name'), 'asdf')
def test_creteTestSample(self):
s1 = bl.createSample(self.sample_type, self.sample_name, self.ber.samples_rack, 1, 0, 0)
self.assertEqual(s1.name, self.sample_name)
self.assertEqual(s1.stype.name, self.sample_type)
self.assertEqual(s1.rack, self.ber.samples_rack)
self.assertEqual(s1.getWell(), (1, 0))
self.assertEqual(s1.getVolume(), 0)
def test__allowPlungerLagCompensation(self):
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0,
1000)
lag = s1._allowPlungerLagCompensation(200, 5)
self.assertEqual(lag, 5)
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0,
200)
lag = s1._allowPlungerLagCompensation(199, 5)
self.assertEqual(lag, 1)
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0,
100)
lag = s1._allowPlungerLagCompensation(100, 0)
self.assertEqual(lag, 0)
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0,
90)
lag = s1._allowPlungerLagCompensation(100, 0)
self.assertEqual(lag, 0)
def test_uptakeLiquid__save_sample_bottom_coord(self):
z_bottom = 120
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0,
100)
self.uptakeLiquid_patched(s1, 100, None, 5, False, False, False,
z_bottom)
saved_z_bottom = s1.getZBottom()
self.assertEqual(saved_z_bottom, z_bottom)
def initReagent(self, reagent):
reagent = reagent.capitalize()
rack_name = self.settings._getRackName(reagent)
rack = self.getRack(rack_name, reagent)
tube_type = self.settings._getTubeType(reagent)
col, row = self.settings._getTubePositionInRack(reagent)
sample_name = reagent + '_tube'
v = self.settings._getReagentVolume(reagent)
tube = bl.createSample(tube_type, sample_name, rack, col, row, v)
return tube
def test_uptakeLiquid__touch_bottom_decision(self,
mock_moveDownUntilPress):
z_bottom = 120 # Mocked Z coordinate of the bottom of the tube
# Sample which has lots of liquid should not be probed for the bottom
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0,
1000)
sample_has_low_volume = s1._isLowVolumeUptakeNeeded(205)
self.uptakeLiquid_patched(s1, 200, None, 5, False, False, False,
z_bottom)
self.assertFalse(sample_has_low_volume)
self.assertFalse(self.ber.moveDownUntilPress.called)
# Regardless of the liquid amount
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0,
1000)
sample_has_low_volume = s1._isLowVolumeUptakeNeeded(205)
self.uptakeLiquid_patched(s1, 20, None, 5, False, False, False,
z_bottom)
self.assertFalse(sample_has_low_volume)
self.assertFalse(self.ber.moveDownUntilPress.called)
def prep_uptakeLiquids_pipetteLagsHandling(self, v_sample,
expected_calls_list,
mock_moveToSample,
mock_moveAxisDelta,
mock_moveDownUntilPress,
mock_movePipetteToVolume):
self.ber.moveDownUntilPress.return_value = 100
v = 100
lag_vol = 5
# Creating a sample
s1 = bl.createSample('eppendorf', 's1', self.ber.samples_rack, 1, 0,
v_sample)
# figuring lag volume down
lag_vol_down = s1._allowPlungerLagCompensation(v, lag_vol)
self.ber.uptakeLiquid(s1, 100, lag_vol=lag_vol) # Tested function
calls_list = self.ber.movePipetteToVolume.mock_calls
for call, expected_call in zip(calls_list, expected_calls_list):
self.assertEqual(call, mock.call(expected_call))
def initReagents(robot, settings):
"""
Return 4 instances of the reagent tubes:
for beads, waste, eluent, ethanol 80%; in this particular order.
The parameters for the tubes (such as volume and location) are also defined according to the sample sheet.
"""
# Beads tube settings
beads_tube_type = returnProtocolParameter(settings, 'Beads tube type')
beads_rack_name = returnProtocolParameter(settings, 'Beads tube rack')
if beads_rack_name == 'samples':
beads_rack = robot.samples_rack
elif beads_rack_name == 'reagents':
beads_rack = robot.reagents_rack
else:
print("wrong Beads tube rack specified in the samplesheet file")
return
beads_col = int(returnProtocolParameter(settings, 'Beads tube column'))
beads_row = int(returnProtocolParameter(settings, 'Beads tube well'))
V_avail_beads = returnProtocolParameter(settings, 'Beads initial volume')
# Initializing beads tube
beads_tube = bl.createSample(beads_tube_type, 'beads', beads_rack,
beads_col, beads_row, V_avail_beads)
# -------------------
# Waste tube settings
waste_tube_type = returnProtocolParameter(settings, 'Waste tube type')
waste_rack_name = returnProtocolParameter(settings, 'Waste tube rack')
if waste_rack_name == 'reagents':
waste_rack = robot.reagents_rack
else:
print("wrong Waste tube rack specified in the samplesheet file")
return
waste_col = 0
waste_row = int(returnProtocolParameter(settings, 'Waste tube position'))
V_waste = returnProtocolParameter(settings, 'Waste volume')
# Initializing waste tube
waste_tube = bl.createSample(waste_tube_type, 'liquid_waste', waste_rack,
waste_col, waste_row, V_waste)
# -------------------
# Eluent tube settings
eluent_tube_type = returnProtocolParameter(settings, 'Eluent tube type')
eluent_rack_name = returnProtocolParameter(settings, 'Eluent tube rack')
if eluent_rack_name == 'reagents':
eluent_rack = robot.reagents_rack
else:
print("wrong Eluent tube rack specified in the samplesheet file")
return
eluent_col = 0
eluent_row = int(returnProtocolParameter(settings, 'Eluent tube position'))
V_avail_eluent = returnProtocolParameter(settings, 'Eluent volume')
# Initializing eluent tube
eluent_tube = bl.createSample(eluent_tube_type, 'eluent', eluent_rack,
eluent_col, eluent_row, V_avail_eluent)
# -------------------
# Ethanol tube settings
ethanol_tube_type = returnProtocolParameter(settings, 'Ethanol tube type')
ethanol_rack_name = returnProtocolParameter(settings, 'Ethanol tube rack')
if ethanol_rack_name == 'reagents':
ethanol_rack = robot.reagents_rack
else:
print("wrong Ethanol tube rack specified in the samplesheet file")
return
ethanol_col = 0
ethanol_row = int(
returnProtocolParameter(settings, 'Ethanol tube position'))
V_avail_ethanol = returnProtocolParameter(settings, 'Ethanol volume')
ethanol80_tube = bl.createSample(ethanol_tube_type, 'EtOH80pct',
ethanol_rack, ethanol_col, ethanol_row,
V_avail_ethanol)
return beads_tube, waste_tube, eluent_tube, ethanol80_tube