def test_two_pools_creation(self):
svc = helpers.mock_artifact_service(two_pool_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
expected = [
['analyte1', 1, 'DNA1', 20.0, 5.3, 26, 'END1'],
['analyte2', 2, 'DNA1', 8.0, 0, 26, 'END1'],
['analyte3', 3, 'DNA1', 6.7, 0, 26, 'END1'],
['analyte4', 9, 'DNA1', 20.0, 5.3, 27, 'END1'],
['analyte5', 10, 'DNA1', 8.0, 0, 27, 'END1'],
['analyte6', 11, 'DNA1', 6.7, 0, 27, 'END1'],
]
# Test:
actual = [[
transfer.aliquot_name, transfer.source_well_index,
transfer.source_plate_pos,
round(transfer.sample_volume, 1),
round(transfer.pipette_buffer_volume,
1), transfer.target_well_index, transfer.target_plate_pos
] for transfer in dilution_scheme.split_row_transfers]
validation_results = list(post_validate_dilution(dilution_scheme))
print_list(expected, "expected")
print_list(actual, "actual")
# Assert:
self.assertEqual(expected, actual)
self.assertEqual(0, len(validation_results))
def test_two_pools_creation(self):
svc = helpers.mock_artifact_service(two_pool_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
expected = [
['analyte1', 1, 'DNA1', 20.0, 5.3, 26, 'END1'],
['analyte2', 2, 'DNA1', 8.0, 0, 26, 'END1'],
['analyte3', 3, 'DNA1', 6.7, 0, 26, 'END1'],
['analyte4', 9, 'DNA1', 20.0, 5.3, 27, 'END1'],
['analyte5', 10, 'DNA1', 8.0, 0, 27, 'END1'],
['analyte6', 11, 'DNA1', 6.7, 0, 27, 'END1'],
]
# Test:
actual = [
[transfer.aliquot_name,
transfer.source_well_index,
transfer.source_plate_pos,
round(transfer.sample_volume, 1),
round(transfer.pipette_buffer_volume, 1),
transfer.target_well_index,
transfer.target_plate_pos] for transfer in dilution_scheme.split_row_transfers
]
validation_results = list(post_validate_dilution(dilution_scheme))
print_list(expected, "expected")
print_list(actual, "actual")
# Assert:
self.assertEqual(expected, actual)
self.assertEqual(0, len(validation_results))
def test_dilution_scheme_source_concentration_zero(self):
def invalid_analyte_set():
pool1 = fake_analyte("cont-id1",
"art-id1", ["sample1", "sample2"],
"pool1",
"B:5",
False,
requested_concentration_nm=100,
requested_volume=20)
return [
(fake_analyte("cont-id1",
"art-id1",
"sample1",
"art-name1",
"D:5",
True,
concentration_nm=0,
volume=100), pool1),
(fake_analyte("cont-id1",
"art-id1",
"sample2",
"art-name1",
"D:5",
True,
concentration_nm=100,
volume=20), pool1),
]
svc = helpers.mock_artifact_service(invalid_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
actual = set(
str(result) for result in pre_validate_dilution(dilution_scheme))
expected = set(["Error: art-name1, source concentration not set."])
self.assertEqual(expected, actual)
def test_dilution_scheme_source_volume_not_set(self):
def invalid_analyte_set():
pool1 = fake_analyte("cont-id1", "art-id1", ["sample1", "sample2"], "pool1", "B:5",
False, requested_concentration_nm=100, requested_volume=20)
return [
(fake_analyte("cont-id1", "art-id1", "sample1", "art-name1", "D:5",
True, concentration_nm=100),
pool1),
(fake_analyte("cont-id1", "art-id1", "sample2", "art-name1", "D:5",
True, concentration_nm=100, volume=20),
pool1),
]
svc = helpers.mock_artifact_service(invalid_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
actual = set(str(result)
for result in pre_validate_dilution(dilution_scheme))
expected = set(["Error: art-name1, source volume is not set."])
self.assertEqual(expected, actual)
def test_single_pool_creation(self):
def pooled_analyte_set():
samples = ["sample1", "sample2", "sample3"]
pool = fake_analyte("cont2", "art4", samples, "Pool1", "B:4",
is_input=False,
requested_concentration_nm=15.0, requested_volume=40.0)
return [
(fake_analyte("cont1", "art1", "sample1", "analyte1", "A:1", is_input=True,
concentration_nm=10.0, volume=300.0),
pool),
(fake_analyte("cont1", "art2", "sample2", "analyte2", "A:2", is_input=True,
concentration_nm=25.0, volume=300.0),
pool),
(fake_analyte("cont1", "art3", "sample3", "analyte3", "A:3", is_input=True,
concentration_nm=30.0, volume=300.0),
pool),
]
svc = helpers.mock_artifact_service(pooled_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
expected = [
['analyte1', 1, 'DNA1', 20.0, 5.3, 26, 'END1'],
['analyte2', 9, 'DNA1', 8.0, 0, 26, 'END1'],
['analyte3', 17, 'DNA1', 6.7, 0, 26, 'END1'],
]
# Test:
actual = [
[transfer.aliquot_name,
transfer.source_well_index,
transfer.source_plate_pos,
round(transfer.sample_volume, 1),
round(transfer.pipette_buffer_volume, 1),
transfer.target_well_index,
transfer.target_plate_pos] for transfer in dilution_scheme.split_row_transfers
]
validation_results = list(post_validate_dilution(dilution_scheme))
# Assert:
self.assertEqual(expected, actual)
self.assertEqual(0, len(validation_results))
def test_scaled_up_warning(self):
def invalid_analyte_set():
samples = ["sample1", "sample2", "sample3"]
pool1 = fake_analyte("cont2", "art4", samples, "Pool1", "B:4",
is_input=False,
requested_concentration_nm=15.0, requested_volume=5.0)
samples = ["sample4", "sample5", "sample6"]
pool2 = fake_analyte("cont2", "art5", samples, "Pool2", "C:4",
is_input=False,
requested_concentration_nm=10.0, requested_volume=40.0)
return [
(fake_analyte("cont1", "art1", "sample1", "analyte1", "A:1", is_input=True,
concentration_nm=10.0, volume=300.0),
pool1),
(fake_analyte("cont1", "art2", "sample2", "analyte2", "B:1", is_input=True,
concentration_nm=25.0, volume=300.0),
pool1),
(fake_analyte("cont1", "art3", "sample3", "analyte3", "C:1", is_input=True,
concentration_nm=30.0, volume=300.0),
pool1),
(fake_analyte("cont1", "art4", "sample4", "analyte4", "A:2", is_input=True,
concentration_nm=10.0, volume=300.0),
pool2),
(fake_analyte("cont1", "art5", "sample5", "analyte5", "B:2", is_input=True,
concentration_nm=25.0, volume=300.0),
pool2),
(fake_analyte("cont1", "art6", "sample6", "analyte6", "C:2", is_input=True,
concentration_nm=30.0, volume=300.0),
pool2),
]
svc = helpers.mock_artifact_service(invalid_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
actual = set(str(result)
for result in post_validate_dilution(dilution_scheme))
expected = set(
["Warning: Pool1, volume has been scaled up due to the min pipetting volume of 2 ul (cont2(B4))."])
self.assertEqual(expected, actual)
def test_too_high_destination_volume_due_to_evaporation(self):
def invalid_analyte_set():
samples = ["sample1", "sample2", "sample3"]
pool1 = fake_analyte("cont2", "art4", samples, "Pool1", "B:4",
is_input=False,
requested_concentration_nm=15, requested_volume=40)
samples = ["sample4", "sample5", "sample6"]
pool2 = fake_analyte("cont2", "art5", samples, "Pool2", "C:4",
is_input=False,
requested_concentration_nm=40, requested_volume=70)
return [
(fake_analyte("cont1", "art1", "sample1", "analyte1", "A:1", is_input=True,
concentration_nm=10, volume=300),
pool1),
(fake_analyte("cont1", "art2", "sample2", "analyte2", "B:1", is_input=True,
concentration_nm=25, volume=300),
pool1),
(fake_analyte("cont1", "art3", "sample3", "analyte3", "C:1", is_input=True,
concentration_nm=30, volume=300),
pool1),
(fake_analyte("cont1", "art4", "sample4", "analyte4", "A:2", is_input=True,
concentration_nm=10, volume=300),
pool2),
(fake_analyte("cont1", "art5", "sample5", "analyte5", "B:2", is_input=True,
concentration_nm=25, volume=300),
pool2),
(fake_analyte("cont1", "art6", "sample6", "analyte6", "C:2", is_input=True,
concentration_nm=30, volume=300),
pool2),
]
svc = helpers.mock_artifact_service(invalid_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
actual = set(str(result)
for result in post_validate_dilution(dilution_scheme))
expected = set(["Error: Pool2, too high destination volume (cont2(C4)).",
"Warning: Pool2, pool has to be evaporated (cont2(C4))."])
self.assertEqual(expected, actual)
def test_scaled_up_and_split_rows(self):
def invalid_analyte_set():
samples = ["sample1", "sample2", "sample3"]
pool1 = fake_analyte("cont2",
"art4",
samples,
"Pool1",
"B:4",
is_input=False,
requested_concentration_nm=15.0,
requested_volume=40.0)
samples = ["sample4", "sample5", "sample6"]
pool2 = fake_analyte("cont2",
"art5",
samples,
"Pool2",
"C:4",
is_input=False,
requested_concentration_nm=7.0,
requested_volume=80.0)
return [
(fake_analyte("cont1",
"art1",
"sample1",
"analyte1",
"A:1",
is_input=True,
concentration_nm=10.0,
volume=300.0), pool1),
(fake_analyte("cont1",
"art2",
"sample2",
"analyte2",
"B:1",
is_input=True,
concentration_nm=25.0,
volume=300.0), pool1),
(fake_analyte("cont1",
"art3",
"sample3",
"analyte3",
"C:1",
is_input=True,
concentration_nm=30.0,
volume=300.0), pool1),
(fake_analyte("cont1",
"art4",
"sample4",
"analyte4",
"A:2",
is_input=True,
concentration_nm=3.0,
volume=300.0), pool2),
(fake_analyte("cont1",
"art5",
"sample5",
"analyte5",
"B:2",
is_input=True,
concentration_nm=25.0,
volume=300.0), pool2),
(fake_analyte("cont1",
"art6",
"sample6",
"analyte6",
"C:2",
is_input=True,
concentration_nm=180.0,
volume=300.0), pool2),
]
svc = helpers.mock_artifact_service(invalid_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
expected = [
['analyte1', 1, 'DNA1', 20.0, 5.3, 26, 'END1'],
['analyte2', 2, 'DNA1', 8.0, 0, 26, 'END1'],
['analyte3', 3, 'DNA1', 6.7, 0, 26, 'END1'],
['analyte4', 9, 'DNA1', 40.0, 17.9, 27, 'END1'],
['analyte4', 9, 'DNA1', 40.0, 0, 27, 'END1'],
['analyte4', 9, 'DNA1', 40.0, 0, 27, 'END1'],
['analyte5', 10, 'DNA1', 14.4, 0, 27, 'END1'],
['analyte6', 11, 'DNA1', 2, 0, 27, 'END1'],
]
# Test:
actual = [[
transfer.aliquot_name, transfer.source_well_index,
transfer.source_plate_pos,
round(transfer.sample_volume, 1),
round(transfer.pipette_buffer_volume,
1), transfer.target_well_index, transfer.target_plate_pos
] for transfer in dilution_scheme.split_row_transfers]
print_list(expected, "expected")
print_list(actual, "actual")
# Assert:
self.assertEqual(expected, actual)
def test_scaled_up_warning(self):
def invalid_analyte_set():
samples = ["sample1", "sample2", "sample3"]
pool1 = fake_analyte("cont2",
"art4",
samples,
"Pool1",
"B:4",
is_input=False,
requested_concentration_nm=15.0,
requested_volume=5.0)
samples = ["sample4", "sample5", "sample6"]
pool2 = fake_analyte("cont2",
"art5",
samples,
"Pool2",
"C:4",
is_input=False,
requested_concentration_nm=10.0,
requested_volume=40.0)
return [
(fake_analyte("cont1",
"art1",
"sample1",
"analyte1",
"A:1",
is_input=True,
concentration_nm=10.0,
volume=300.0), pool1),
(fake_analyte("cont1",
"art2",
"sample2",
"analyte2",
"B:1",
is_input=True,
concentration_nm=25.0,
volume=300.0), pool1),
(fake_analyte("cont1",
"art3",
"sample3",
"analyte3",
"C:1",
is_input=True,
concentration_nm=30.0,
volume=300.0), pool1),
(fake_analyte("cont1",
"art4",
"sample4",
"analyte4",
"A:2",
is_input=True,
concentration_nm=10.0,
volume=300.0), pool2),
(fake_analyte("cont1",
"art5",
"sample5",
"analyte5",
"B:2",
is_input=True,
concentration_nm=25.0,
volume=300.0), pool2),
(fake_analyte("cont1",
"art6",
"sample6",
"analyte6",
"C:2",
is_input=True,
concentration_nm=30.0,
volume=300.0), pool2),
]
svc = helpers.mock_artifact_service(invalid_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
actual = set(
str(result) for result in post_validate_dilution(dilution_scheme))
expected = set([
"Warning: Pool1, volume has been scaled up due to the min pipetting volume of 2 ul (cont2(B4))."
])
self.assertEqual(expected, actual)
def test_too_high_destination_volume_due_to_evaporation(self):
def invalid_analyte_set():
samples = ["sample1", "sample2", "sample3"]
pool1 = fake_analyte("cont2",
"art4",
samples,
"Pool1",
"B:4",
is_input=False,
requested_concentration_nm=15,
requested_volume=40)
samples = ["sample4", "sample5", "sample6"]
pool2 = fake_analyte("cont2",
"art5",
samples,
"Pool2",
"C:4",
is_input=False,
requested_concentration_nm=40,
requested_volume=70)
return [
(fake_analyte("cont1",
"art1",
"sample1",
"analyte1",
"A:1",
is_input=True,
concentration_nm=10,
volume=300), pool1),
(fake_analyte("cont1",
"art2",
"sample2",
"analyte2",
"B:1",
is_input=True,
concentration_nm=25,
volume=300), pool1),
(fake_analyte("cont1",
"art3",
"sample3",
"analyte3",
"C:1",
is_input=True,
concentration_nm=30,
volume=300), pool1),
(fake_analyte("cont1",
"art4",
"sample4",
"analyte4",
"A:2",
is_input=True,
concentration_nm=10,
volume=300), pool2),
(fake_analyte("cont1",
"art5",
"sample5",
"analyte5",
"B:2",
is_input=True,
concentration_nm=25,
volume=300), pool2),
(fake_analyte("cont1",
"art6",
"sample6",
"analyte6",
"C:2",
is_input=True,
concentration_nm=30,
volume=300), pool2),
]
svc = helpers.mock_artifact_service(invalid_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
actual = set(
str(result) for result in post_validate_dilution(dilution_scheme))
expected = set([
"Error: Pool2, too high destination volume (cont2(C4)).",
"Warning: Pool2, pool has to be evaporated (cont2(C4))."
])
self.assertEqual(expected, actual)
def test_single_pool_creation(self):
def pooled_analyte_set():
samples = ["sample1", "sample2", "sample3"]
pool = fake_analyte("cont2",
"art4",
samples,
"Pool1",
"B:4",
is_input=False,
requested_concentration_nm=15.0,
requested_volume=40.0)
return [
(fake_analyte("cont1",
"art1",
"sample1",
"analyte1",
"A:1",
is_input=True,
concentration_nm=10.0,
volume=300.0), pool),
(fake_analyte("cont1",
"art2",
"sample2",
"analyte2",
"A:2",
is_input=True,
concentration_nm=25.0,
volume=300.0), pool),
(fake_analyte("cont1",
"art3",
"sample3",
"analyte3",
"A:3",
is_input=True,
concentration_nm=30.0,
volume=300.0), pool),
]
svc = helpers.mock_artifact_service(pooled_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
expected = [
['analyte1', 1, 'DNA1', 20.0, 5.3, 26, 'END1'],
['analyte2', 9, 'DNA1', 8.0, 0, 26, 'END1'],
['analyte3', 17, 'DNA1', 6.7, 0, 26, 'END1'],
]
# Test:
actual = [[
transfer.aliquot_name, transfer.source_well_index,
transfer.source_plate_pos,
round(transfer.sample_volume, 1),
round(transfer.pipette_buffer_volume,
1), transfer.target_well_index, transfer.target_plate_pos
] for transfer in dilution_scheme.split_row_transfers]
validation_results = list(post_validate_dilution(dilution_scheme))
# Assert:
self.assertEqual(expected, actual)
self.assertEqual(0, len(validation_results))
def test_scaled_up_and_split_rows(self):
def invalid_analyte_set():
samples = ["sample1", "sample2", "sample3"]
pool1 = fake_analyte("cont2", "art4", samples, "Pool1", "B:4",
is_input=False,
requested_concentration_nm=15.0, requested_volume=40.0)
samples = ["sample4", "sample5", "sample6"]
pool2 = fake_analyte("cont2", "art5", samples, "Pool2", "C:4",
is_input=False,
requested_concentration_nm=7.0, requested_volume=80.0)
return [
(fake_analyte("cont1", "art1", "sample1", "analyte1", "A:1", is_input=True,
concentration_nm=10.0, volume=300.0),
pool1),
(fake_analyte("cont1", "art2", "sample2", "analyte2", "B:1", is_input=True,
concentration_nm=25.0, volume=300.0),
pool1),
(fake_analyte("cont1", "art3", "sample3", "analyte3", "C:1", is_input=True,
concentration_nm=30.0, volume=300.0),
pool1),
(fake_analyte("cont1", "art4", "sample4", "analyte4", "A:2", is_input=True,
concentration_nm=3.0, volume=300.0),
pool2),
(fake_analyte("cont1", "art5", "sample5", "analyte5", "B:2", is_input=True,
concentration_nm=25.0, volume=300.0),
pool2),
(fake_analyte("cont1", "art6", "sample6", "analyte6", "C:2", is_input=True,
concentration_nm=180.0, volume=300.0),
pool2),
]
svc = helpers.mock_artifact_service(invalid_analyte_set)
dilution_scheme = self._default_dilution_scheme(svc)
expected = [
['analyte1', 1, 'DNA1', 20.0, 5.3, 26, 'END1'],
['analyte2', 2, 'DNA1', 8.0, 0, 26, 'END1'],
['analyte3', 3, 'DNA1', 6.7, 0, 26, 'END1'],
['analyte4', 9, 'DNA1', 40.0, 17.9, 27, 'END1'],
['analyte4', 9, 'DNA1', 40.0, 0, 27, 'END1'],
['analyte4', 9, 'DNA1', 40.0, 0, 27, 'END1'],
['analyte5', 10, 'DNA1', 14.4, 0, 27, 'END1'],
['analyte6', 11, 'DNA1', 2, 0, 27, 'END1'],
]
# Test:
actual = [
[transfer.aliquot_name,
transfer.source_well_index,
transfer.source_plate_pos,
round(transfer.sample_volume, 1),
round(transfer.pipette_buffer_volume, 1),
transfer.target_well_index,
transfer.target_plate_pos] for transfer in dilution_scheme.split_row_transfers
]
print_list(expected, "expected")
print_list(actual, "actual")
# Assert:
self.assertEqual(expected, actual)