def test_primer_set_composition_attributes(self):
obs = PrimerSetComposition(1)
self.assertEqual(obs.container, Well(1))
self.assertEqual(obs.total_volume, 0)
self.assertIsNone(obs.notes)
self.assertEqual(obs.composition_id, 1)
self.assertEqual(obs.barcode, 'TCCCTTGTCTCC')
def test_primer_composition_attributes(self):
obs = PrimerComposition(1)
self.assertEqual(obs.container, Well(1537))
self.assertEqual(obs.total_volume, 10)
self.assertIsNone(obs.notes)
self.assertEqual(obs.composition_id, 1537)
self.assertEqual(obs.primer_set_composition, PrimerSetComposition(1))
def test_get_next_combos(self):
tester = ShotgunPrimerSet(1)
self.assertEqual(tester.current_combo_index, 384)
with self.assertRaises(ValueError):
tester.get_next_combos(0)
with self.assertRaises(ValueError):
tester.get_next_combos(150000)
obs = tester.get_next_combos(5)
self.assertEqual(tester.current_combo_index, 389)
self.assertEqual(len(obs), 5)
exp = [(PrimerSetComposition(769), PrimerSetComposition(1155)),
(PrimerSetComposition(771), PrimerSetComposition(1157)),
(PrimerSetComposition(773), PrimerSetComposition(1159)),
(PrimerSetComposition(775), PrimerSetComposition(1161)),
(PrimerSetComposition(777), PrimerSetComposition(1163))]
self.assertEqual(obs, exp)
def test_get_next_combos(self):
tester = ShotgunPrimerSet(1)
# NOTE: 380 instead of 384 because the test sample plate contains 1
# empty well. When the plate is collapsed 4 times into a 384-well plate
# this results with 4 empty wells not included in library prep
self.assertEqual(tester.current_combo_index, 380)
with self.assertRaises(ValueError):
tester.get_next_combos(0)
with self.assertRaises(ValueError):
tester.get_next_combos(150000)
obs = tester.get_next_combos(5)
self.assertEqual(tester.current_combo_index, 385)
self.assertEqual(len(obs), 5)
exp = [(PrimerSetComposition(1146), PrimerSetComposition(1530)),
(PrimerSetComposition(1148), PrimerSetComposition(1532)),
(PrimerSetComposition(1150), PrimerSetComposition(1534)),
(PrimerSetComposition(1152), PrimerSetComposition(1536)),
(PrimerSetComposition(769), PrimerSetComposition(1155))]
self.assertEqual(obs, exp)
def test_composition_factory(self):
self.assertEqual(Composition.factory(3073), ReagentComposition(1))
self.assertEqual(Composition.factory(1537), PrimerComposition(1))
self.assertEqual(Composition.factory(1), PrimerSetComposition(1))
self.assertEqual(Composition.factory(3081), SampleComposition(1))
self.assertEqual(Composition.factory(3082), GDNAComposition(1))
self.assertEqual(Composition.factory(3083),
LibraryPrep16SComposition(1))
self.assertEqual(Composition.factory(3085),
NormalizedGDNAComposition(1))
self.assertEqual(Composition.factory(3086),
LibraryPrepShotgunComposition(1))
self.assertEqual(Composition.factory(3078), PoolComposition(1))
def test_primer_composition_attributes(self):
obs = PrimerComposition(1)
self.assertEqual(obs.container, Well(1537))
self.assertEqual(obs.total_volume, 10)
self.assertIsNone(obs.notes)
# NB: the fact that the composition id is 1538 and the well id is 1537
# is not a mistake. There is a placeholder composition (for "Not
# Applicable", supporting externally extracted DNA) added in
# db_patch_manual.sql, before populate_test_db.sql is run to create the
# records being tested here--but that composition is "stored" in a
# placeholder TUBE rather than a placeholder WELL, so there is no
# analogous extra well record.
self.assertEqual(obs.composition_id, 1538)
self.assertEqual(obs.primer_set_composition, PrimerSetComposition(1))
self.assertIsNone(obs.study)