def post(self): user = self.current_user plate_config_id = self.get_argument('plate_configuration') plate_ext_id = self.get_argument('plate_name') spp = SamplePlatingProcess.create( user, PlateConfiguration(plate_config_id), plate_ext_id) self.write({'plate_id': spp.plate.id, 'process_id': spp.id})
def plate_map_handler_get_request(plate_id): process_id = None if plate_id is not None: plate = _get_plate(plate_id) # Access the first well to get the process id - all wells have the same well = plate.get_well(1, 1) process_id = well.latest_process.id plate_confs = [[pc.id, pc.description, pc.num_rows, pc.num_columns] for pc in PlateConfiguration.iter()] return {'plate_confs': plate_confs, 'plate_id': plate_id, 'process_id': process_id}
def test_create(self): plate_conf = PlateConfiguration.create('96-well Test desc', 8, 12) obs = Plate.create('New plate', plate_conf) self.assertEqual(obs.external_id, 'New plate') self.assertEqual(obs.plate_configuration, plate_conf) self.assertFalse(obs.discarded) self.assertIsNone(obs.notes) # This is a weird case and it should never happen in normal execution # of the code: the plate has been created without any well, hence all # the None values. In reality, all the plate creation is handled # by one of the Process classes, which ensures the creation of all # the wells. self.assertEqual(obs.layout, [[None] * 12] * 8)
def plate_map_handler_get_request(process_id): plate_id = None if process_id is not None: try: process = SamplePlatingProcess(process_id) except LabmanUnknownIdError: raise HTTPError(404, reason="Plating process %s doesn't exist" % process_id) plate_id = process.plate.id plate_confs = [[pc.id, pc.description, pc.num_rows, pc.num_columns] for pc in PlateConfiguration.iter() if 'template' not in pc.description] return {'plate_confs': plate_confs, 'plate_id': plate_id, 'process_id': process_id}
def test_get_previously_plated_wells(self): tester = Plate(21) three_plates_list = [Plate(27), Plate(30), Plate(33)] exp = {Well(3073): three_plates_list, Well(3079): three_plates_list, Well(3085): three_plates_list, Well(3091): three_plates_list, Well(3097): three_plates_list, Well(3103): three_plates_list, Well(3121): three_plates_list, Well(3127): three_plates_list, Well(3133): three_plates_list, Well(3139): three_plates_list, Well(3145): three_plates_list, Well(3151): three_plates_list, Well(3169): three_plates_list, Well(3175): three_plates_list, Well(3181): three_plates_list, Well(3187): three_plates_list, Well(3193): three_plates_list, Well(3199): three_plates_list, Well(3217): three_plates_list, Well(3223): three_plates_list, Well(3229): three_plates_list, Well(3235): three_plates_list, Well(3241): three_plates_list, Well(3247): three_plates_list, Well(3265): three_plates_list, Well(3271): three_plates_list, Well(3277): three_plates_list, Well(3283): three_plates_list, Well(3289): three_plates_list, Well(3295): three_plates_list, Well(3313): three_plates_list, Well(3319): three_plates_list, Well(3325): three_plates_list, Well(3331): three_plates_list, Well(3337): three_plates_list, Well(3343): three_plates_list, Well(3361): three_plates_list, Well(3367): three_plates_list, Well(3373): three_plates_list, Well(3379): three_plates_list, Well(3385): three_plates_list, Well(3391): three_plates_list, Well(3409): three_plates_list, Well(3415): three_plates_list, Well(3421): three_plates_list, Well(3427): three_plates_list, Well(3433): three_plates_list, Well(3439): three_plates_list, Well(3457): three_plates_list, Well(3463): three_plates_list, Well(3469): three_plates_list, Well(3475): three_plates_list, Well(3481): three_plates_list, Well(3487): three_plates_list, Well(3505): three_plates_list, Well(3511): three_plates_list, Well(3517): three_plates_list, Well(3523): three_plates_list, Well(3529): three_plates_list, Well(3535): three_plates_list, Well(3553): three_plates_list, Well(3559): three_plates_list, Well(3565): three_plates_list, Well(3571): three_plates_list, Well(3577): three_plates_list, Well(3583): three_plates_list, Well(3601): three_plates_list, Well(3607): three_plates_list, Well(3613): three_plates_list, Well(3619): three_plates_list, Well(3625): three_plates_list} obs = tester.get_previously_plated_wells() self.assertEqual(obs, exp) # Create another plate and put a sample on it that isn't anywhere else spp = SamplePlatingProcess.create( User('*****@*****.**'), PlateConfiguration(1), 'New Plate For Prev') spp.update_well(1, 1, '1.SKM1.640184') obs = spp.plate.get_previously_plated_wells() self.assertEqual(obs, {})
def test_properties(self): # Plate 21 - Defined in the test DB tester = Plate(21) self.assertEqual(tester.external_id, 'Test plate 1') self.assertEqual(tester.plate_configuration, PlateConfiguration(1)) self.assertFalse(tester.discarded) self.assertIsNone(tester.notes) obs_layout = tester.layout self.assertEqual(len(obs_layout), 8) for row in obs_layout: self.assertEqual(len(row), 12) # Test changing the name of the plate tester.external_id = 'Some new name' self.assertEqual(tester.external_id, 'Some new name') tester.external_id = 'Test plate 1' self.assertEqual(tester.external_id, 'Test plate 1')
def test_iter(self): obs = PlateConfiguration.iter() self.assertIsInstance(obs, GeneratorType) obs = list(obs) # Since we can't ensure the test order between this test and # test_create, we check both lengths, but we only check the content # of the first 5 elements self.assertIn(len(obs), [5, 6]) exp = [PlateConfiguration(1), PlateConfiguration(2), PlateConfiguration(3), PlateConfiguration(4), PlateConfiguration(5)] self.assertEqual(obs[:5], exp)
def test_get_previously_plated_wells(self): tester = Plate(21) self.assertEqual(tester.get_previously_plated_wells(), {}) # Create another plate and plate some samples in it spp = SamplePlatingProcess.create( User('*****@*****.**'), PlateConfiguration(1), 'New Plate For Prev') spp.update_well(1, 1, '1.SKD1.640179') exp = {} plate = spp.plate exp[Well(3208)] = [plate] exp[Well(3388)] = [plate] exp[Well(3568)] = [plate] exp[Well(3748)] = [plate] exp[Well(3928)] = [plate] exp[Well(4108)] = [plate] obs = tester.get_previously_plated_wells() self.assertEqual(obs, exp)
def get_target_plate_configuration(is_96): plate_configs = list(PlateConfiguration.iter()) plate_config = None if is_96: target = '96-well deep-well plate' else: target = '384-well microtiter plate' for pc in plate_configs: if pc.description == target: plate_config = pc break if plate_config is None: raise ValueError("Unable to identify a plate of type: %s" % target) return plate_config
def create_sample_plate_process(user, samples): plate_config = PlateConfiguration(1) num_rows = plate_config.num_rows num_cols = plate_config.num_columns sp_process = SamplePlatingProcess.create(user, plate_config, 'Test plate %s' % datetime.now()) # Plate the samples for idx, sample in enumerate(samples): i = int(idx / num_cols) + 1 j = (idx % num_cols) + 1 # Make sure that the user didn't pass more samples than wells if i > num_rows: break sp_process.update_well(i, j, sample) sample_plate = sp_process.plate return sp_process, sample_plate
def test_create(self): obs = PlateConfiguration.create('96-well Test description', 8, 12) self.assertEqual(obs.description, '96-well Test description') self.assertEqual(obs.num_rows, 8) self.assertEqual(obs.num_columns, 12)
def test_properties(self): # Plate 21 - Defined in the test DB tester = Plate(21) self.assertEqual(tester.external_id, 'Test plate 1') self.assertEqual(tester.plate_configuration, PlateConfiguration(1)) self.assertFalse(tester.discarded) self.assertIsNone(tester.notes) obs_layout = tester.layout self.assertEqual(len(obs_layout), 8) for row in obs_layout: self.assertEqual(len(row), 12) self.assertEqual(tester.studies, {Study(1)}) self.assertIsNone(tester.quantification_process) self.assertEqual(tester.process, SamplePlatingProcess(10)) # Test changing the name of the plate tester.external_id = 'Some new name' self.assertEqual(tester.external_id, 'Some new name') tester.external_id = 'Test plate 1' self.assertEqual(tester.external_id, 'Test plate 1') self.assertEqual( Plate(23).quantification_process, QuantificationProcess(1)) self.assertEqual(Plate(22).process, GDNAExtractionProcess(1)) exp = { '1.SKB1.640202': [ Well(3073), Well(3253), Well(3433), Well(3613), Well(3793), Well(3973) ], '1.SKB2.640194': [ Well(3088), Well(3268), Well(3448), Well(3628), Well(3808), Well(3988) ], '1.SKB3.640195': [ Well(3103), Well(3283), Well(3463), Well(3643), Well(3823), Well(4003) ], '1.SKB4.640189': [ Well(3118), Well(3298), Well(3478), Well(3658), Well(3838), Well(4018) ], '1.SKB5.640181': [ Well(3133), Well(3313), Well(3493), Well(3673), Well(3853), Well(4033) ], '1.SKB6.640176': [ Well(3148), Well(3328), Well(3508), Well(3688), Well(3868), Well(4048) ], '1.SKB7.640196': [ Well(3163), Well(3343), Well(3523), Well(3703), Well(3883), Well(4063) ], '1.SKB8.640193': [ Well(3178), Well(3358), Well(3538), Well(3718), Well(3898), Well(4078) ], '1.SKB9.640200': [ Well(3193), Well(3373), Well(3553), Well(3733), Well(3913), Well(4093) ], '1.SKD1.640179': [ Well(3208), Well(3388), Well(3568), Well(3748), Well(3928), Well(4108) ], '1.SKD2.640178': [ Well(3223), Well(3403), Well(3583), Well(3763), Well(3943), Well(4123) ], '1.SKD3.640198': [ Well(3238), Well(3418), Well(3598), Well(3778), Well(3958), Well(4138) ] } self.assertEqual(tester.duplicates, exp)
def test_properties(self): # Plate 21 - Defined in the test DB tester = Plate(21) self.assertEqual(tester.external_id, 'Test plate 1') self.assertEqual(tester.plate_configuration, PlateConfiguration(1)) self.assertFalse(tester.discarded) tester.discarded = True self.assertTrue(tester.discarded) self.assertIsNone(tester.notes) obs_layout = tester.layout self.assertEqual(len(obs_layout), 8) for row in obs_layout: self.assertEqual(len(row), 12) self.assertEqual(tester.studies, {Study(1)}) self.assertIsNone(tester.quantification_process) self.assertEqual(tester.process, SamplePlatingProcess(10)) # Test changing the name of the plate tester.external_id = 'Some new name' self.assertEqual(tester.external_id, 'Some new name') tester.external_id = 'Test plate 1' self.assertEqual(tester.external_id, 'Test plate 1') self.assertEqual( Plate(23).quantification_process, QuantificationProcess(1)) self.assertEqual(Plate(22).process, GDNAExtractionProcess(1)) exp = { '1.SKB1.640202': [[Well(3073), '1.SKB1.640202.21.A1'], [Well(3253), '1.SKB1.640202.21.B1'], [Well(3433), '1.SKB1.640202.21.C1'], [Well(3613), '1.SKB1.640202.21.D1'], [Well(3793), '1.SKB1.640202.21.E1'], [Well(3973), '1.SKB1.640202.21.F1']], '1.SKB2.640194': [[Well(3088), '1.SKB2.640194.21.A2'], [Well(3268), '1.SKB2.640194.21.B2'], [Well(3448), '1.SKB2.640194.21.C2'], [Well(3628), '1.SKB2.640194.21.D2'], [Well(3808), '1.SKB2.640194.21.E2'], [Well(3988), '1.SKB2.640194.21.F2']], '1.SKB3.640195': [[Well(3103), '1.SKB3.640195.21.A3'], [Well(3283), '1.SKB3.640195.21.B3'], [Well(3463), '1.SKB3.640195.21.C3'], [Well(3643), '1.SKB3.640195.21.D3'], [Well(3823), '1.SKB3.640195.21.E3'], [Well(4003), '1.SKB3.640195.21.F3']], '1.SKB4.640189': [[Well(3118), '1.SKB4.640189.21.A4'], [Well(3298), '1.SKB4.640189.21.B4'], [Well(3478), '1.SKB4.640189.21.C4'], [Well(3658), '1.SKB4.640189.21.D4'], [Well(3838), '1.SKB4.640189.21.E4'], [Well(4018), '1.SKB4.640189.21.F4']], '1.SKB5.640181': [[Well(3133), '1.SKB5.640181.21.A5'], [Well(3313), '1.SKB5.640181.21.B5'], [Well(3493), '1.SKB5.640181.21.C5'], [Well(3673), '1.SKB5.640181.21.D5'], [Well(3853), '1.SKB5.640181.21.E5'], [Well(4033), '1.SKB5.640181.21.F5']], '1.SKB6.640176': [[Well(3148), '1.SKB6.640176.21.A6'], [Well(3328), '1.SKB6.640176.21.B6'], [Well(3508), '1.SKB6.640176.21.C6'], [Well(3688), '1.SKB6.640176.21.D6'], [Well(3868), '1.SKB6.640176.21.E6'], [Well(4048), '1.SKB6.640176.21.F6']], '1.SKB7.640196': [[Well(3163), '1.SKB7.640196.21.A7'], [Well(3343), '1.SKB7.640196.21.B7'], [Well(3523), '1.SKB7.640196.21.C7'], [Well(3703), '1.SKB7.640196.21.D7'], [Well(3883), '1.SKB7.640196.21.E7'], [Well(4063), '1.SKB7.640196.21.F7']], '1.SKB8.640193': [[Well(3178), '1.SKB8.640193.21.A8'], [Well(3358), '1.SKB8.640193.21.B8'], [Well(3538), '1.SKB8.640193.21.C8'], [Well(3718), '1.SKB8.640193.21.D8'], [Well(3898), '1.SKB8.640193.21.E8'], [Well(4078), '1.SKB8.640193.21.F8']], '1.SKB9.640200': [[Well(3193), '1.SKB9.640200.21.A9'], [Well(3373), '1.SKB9.640200.21.B9'], [Well(3553), '1.SKB9.640200.21.C9'], [Well(3733), '1.SKB9.640200.21.D9'], [Well(3913), '1.SKB9.640200.21.E9'], [Well(4093), '1.SKB9.640200.21.F9']], '1.SKD1.640179': [[Well(3208), '1.SKD1.640179.21.A10'], [Well(3388), '1.SKD1.640179.21.B10'], [Well(3568), '1.SKD1.640179.21.C10'], [Well(3748), '1.SKD1.640179.21.D10'], [Well(3928), '1.SKD1.640179.21.E10'], [Well(4108), '1.SKD1.640179.21.F10']], '1.SKD2.640178': [[Well(3223), '1.SKD2.640178.21.A11'], [Well(3403), '1.SKD2.640178.21.B11'], [Well(3583), '1.SKD2.640178.21.C11'], [Well(3763), '1.SKD2.640178.21.D11'], [Well(3943), '1.SKD2.640178.21.E11'], [Well(4123), '1.SKD2.640178.21.F11']], '1.SKD3.640198': [[Well(3238), '1.SKD3.640198.21.A12'], [Well(3418), '1.SKD3.640198.21.B12'], [Well(3598), '1.SKD3.640198.21.C12'], [Well(3778), '1.SKD3.640198.21.D12'], [Well(3958), '1.SKD3.640198.21.E12'], [Well(4138), '1.SKD3.640198.21.F12']] } self.assertEqual(tester.duplicates, exp) self.assertEqual(tester.unknown_samples, []) exp = tester.get_well(1, 1) exp.composition.update('Unknown') self.assertEqual(tester.unknown_samples, [exp]) exp.composition.update('1.SKB1.640202')
def test_properties(self): # Plate 21 - Defined in the test DB tester = Plate(21) self.assertEqual(tester.external_id, 'Test plate 1') self.assertEqual(tester.plate_configuration, PlateConfiguration(1)) self.assertFalse(tester.discarded) tester.discarded = True self.assertTrue(tester.discarded) self.assertIsNone(tester.notes) obs_layout = tester.layout self.assertEqual(len(obs_layout), 8) for row in obs_layout: self.assertEqual(len(row), 12) self.assertEqual(tester.studies, {Study(1)}) self.assertListEqual(tester.quantification_processes, []) self.assertEqual(tester.process, SamplePlatingProcess(10)) # Test changing the name of the plate tester.external_id = 'Some new name' self.assertEqual(tester.external_id, 'Some new name') tester.external_id = 'Test plate 1' self.assertEqual(tester.external_id, 'Test plate 1') self.assertEqual(len(Plate(23).quantification_processes), 1) self.assertEqual( Plate(23).quantification_processes[0], QuantificationProcess(1)) self.assertEqual(Plate(22).process, GDNAExtractionProcess(1)) exp = { '1.SKB1.640202': [[Well(3073), '1.SKB1.640202.21.A1'], [Well(3121), '1.SKB1.640202.21.A2'], [Well(3169), '1.SKB1.640202.21.A3'], [Well(3217), '1.SKB1.640202.21.A4'], [Well(3265), '1.SKB1.640202.21.A5'], [Well(3313), '1.SKB1.640202.21.A6'], [Well(3361), '1.SKB1.640202.21.A7'], [Well(3409), '1.SKB1.640202.21.A8'], [Well(3457), '1.SKB1.640202.21.A9'], [Well(3505), '1.SKB1.640202.21.A10'], [Well(3553), '1.SKB1.640202.21.A11'], [Well(3601), '1.SKB1.640202.21.A12']], '1.SKB2.640194': [[Well(3079), '1.SKB2.640194.21.B1'], [Well(3127), '1.SKB2.640194.21.B2'], [Well(3175), '1.SKB2.640194.21.B3'], [Well(3223), '1.SKB2.640194.21.B4'], [Well(3271), '1.SKB2.640194.21.B5'], [Well(3319), '1.SKB2.640194.21.B6'], [Well(3367), '1.SKB2.640194.21.B7'], [Well(3415), '1.SKB2.640194.21.B8'], [Well(3463), '1.SKB2.640194.21.B9'], [Well(3511), '1.SKB2.640194.21.B10'], [Well(3559), '1.SKB2.640194.21.B11'], [Well(3607), '1.SKB2.640194.21.B12']], '1.SKB3.640195': [[Well(3085), '1.SKB3.640195.21.C1'], [Well(3133), '1.SKB3.640195.21.C2'], [Well(3181), '1.SKB3.640195.21.C3'], [Well(3229), '1.SKB3.640195.21.C4'], [Well(3277), '1.SKB3.640195.21.C5'], [Well(3325), '1.SKB3.640195.21.C6'], [Well(3373), '1.SKB3.640195.21.C7'], [Well(3421), '1.SKB3.640195.21.C8'], [Well(3469), '1.SKB3.640195.21.C9'], [Well(3517), '1.SKB3.640195.21.C10'], [Well(3565), '1.SKB3.640195.21.C11'], [Well(3613), '1.SKB3.640195.21.C12']], '1.SKB4.640189': [[Well(3091), '1.SKB4.640189.21.D1'], [Well(3139), '1.SKB4.640189.21.D2'], [Well(3187), '1.SKB4.640189.21.D3'], [Well(3235), '1.SKB4.640189.21.D4'], [Well(3283), '1.SKB4.640189.21.D5'], [Well(3331), '1.SKB4.640189.21.D6'], [Well(3379), '1.SKB4.640189.21.D7'], [Well(3427), '1.SKB4.640189.21.D8'], [Well(3475), '1.SKB4.640189.21.D9'], [Well(3523), '1.SKB4.640189.21.D10'], [Well(3571), '1.SKB4.640189.21.D11'], [Well(3619), '1.SKB4.640189.21.D12']], '1.SKB5.640181': [[Well(3097), '1.SKB5.640181.21.E1'], [Well(3145), '1.SKB5.640181.21.E2'], [Well(3193), '1.SKB5.640181.21.E3'], [Well(3241), '1.SKB5.640181.21.E4'], [Well(3289), '1.SKB5.640181.21.E5'], [Well(3337), '1.SKB5.640181.21.E6'], [Well(3385), '1.SKB5.640181.21.E7'], [Well(3433), '1.SKB5.640181.21.E8'], [Well(3481), '1.SKB5.640181.21.E9'], [Well(3529), '1.SKB5.640181.21.E10'], [Well(3577), '1.SKB5.640181.21.E11'], [Well(3625), '1.SKB5.640181.21.E12']], '1.SKB6.640176': [[Well(3103), '1.SKB6.640176.21.F1'], [Well(3151), '1.SKB6.640176.21.F2'], [Well(3199), '1.SKB6.640176.21.F3'], [Well(3247), '1.SKB6.640176.21.F4'], [Well(3295), '1.SKB6.640176.21.F5'], [Well(3343), '1.SKB6.640176.21.F6'], [Well(3391), '1.SKB6.640176.21.F7'], [Well(3439), '1.SKB6.640176.21.F8'], [Well(3487), '1.SKB6.640176.21.F9'], [Well(3535), '1.SKB6.640176.21.F10'], [Well(3583), '1.SKB6.640176.21.F11'], [Well(3631), '1.SKB6.640176.21.F12']] } self.assertEqual(tester.duplicates, exp) self.assertEqual(tester.unknown_samples, []) exp = tester.get_well(1, 1) exp.composition.update('Unknown') self.assertEqual(tester.unknown_samples, [exp]) exp.composition.update('1.SKB1.640202') # test that the quantification_processes attribute correctly # orders multiple processes in order from oldest to newest tester2 = Plate(26) self.assertEqual(len(tester2.quantification_processes), 2) self.assertEqual( tester2.quantification_processes[0].date, datetime.strptime("2017-10-25 19:10:25-0700", '%Y-%m-%d %H:%M:%S%z')) self.assertEqual( tester2.quantification_processes[1].date, datetime.strptime("2017-10-26 03:10:25-0700", '%Y-%m-%d %H:%M:%S%z'))