def get(self):
plate_ids = self.get_arguments('plate_id')
process_id = self.get_argument('process_id', None)
kingfisher = None
epmotion = None
epmotion_tool = None
extraction_kit = None
sample_plate = None
externally_extracted = False
volume = None
ext_date = None
notes = None
if process_id is not None:
try:
process = GDNAExtractionProcess(process_id)
except LabmanUnknownIdError:
raise HTTPError(404,
reason="Extraction process %s doesn't exist" %
process_id)
kingfisher = process.kingfisher.id
epmotion = process.epmotion.id
epmotion_tool = process.epmotion_tool.id
extraction_kit = process.extraction_kit.external_lot_id
sample_plate = process.sample_plate.id
externally_extracted = process.externally_extracted
volume = process.volume
ext_date = process.date.strftime(process.get_date_format())
notes = process.notes
ep_robots = Equipment.list_equipment('EpMotion')
kf_robots = Equipment.list_equipment('King Fisher')
tools = Equipment.list_equipment('tm 1000 8 channel pipette head')
self.render('extraction.html',
plate_ids=plate_ids,
kf_robots=kf_robots,
ep_robots=ep_robots,
tools=tools,
process_id=process_id,
kingfisher=kingfisher,
epmotion=epmotion,
epmotion_tool=epmotion_tool,
extraction_kit=extraction_kit,
sample_plate=sample_plate,
externally_extracted=externally_extracted,
volume=volume,
extraction_date=ext_date,
notes=notes)
def test_gDNA_composition_attributes(self):
obs = GDNAComposition(1)
self.assertEqual(obs.sample_composition, SampleComposition(1))
self.assertEqual(obs.upstream_process, GDNAExtractionProcess(1))
self.assertEqual(obs.container, Well(3074))
self.assertEqual(obs.total_volume, 10)
self.assertIsNone(obs.notes)
self.assertEqual(obs.composition_id, 3082)
def create_gdna_extraction_process(user, plate):
kingfisher = Equipment(11)
epmotion = Equipment(6)
epmotion_tool = Equipment(15)
extraction_kit = ReagentComposition(1)
ext_process = GDNAExtractionProcess.create(
user, plate, kingfisher, epmotion, epmotion_tool, extraction_kit, 100,
'GDNA test plate %s' % datetime.now())
gdna_plate = ext_process.plates[0]
return ext_process, gdna_plate
def post(self):
robot = self.get_argument('robot')
tool = self.get_argument('tool')
kit = self.get_argument('kit')
plates = self.get_argument('plates')
volume = self.get_argument('volume')
plates = [Plate(pid) for pid in json_decode(plates)]
process = GDNAExtractionProcess.create(
self.current_user, Equipment(robot), Equipment(tool),
ReagentComposition.from_external_id(kit), plates, volume)
self.write({'process': process.id})
def post(self):
plates_info = self.get_argument('plates_info')
extraction_date = self.get_argument('extraction_date')
volume = self.get_argument('volume')
month, day, year = map(int, extraction_date.split('/'))
extraction_date = date(year, month, day)
plates_info = [
(Plate(pid), Equipment(kf), Equipment(ep), Equipment(ept),
ReagentComposition.from_external_id(kit), p_name)
for pid, kf, ep, ept, kit, p_name in json_decode(plates_info)
]
process = GDNAExtractionProcess.create(self.current_user,
plates_info,
volume,
extraction_date=extraction_date)
self.write({'process': process.id})
def post(self):
plates_info = self.get_argument('plates_info')
extraction_date = self.get_argument('extraction_date')
volume = self.get_argument('volume')
month, day, year = map(int, extraction_date.split('/'))
extraction_date = date(year, month, day)
# We create one process per plate
processes = []
for pid, ee, kf, ep, ept, kit, p_name, nt in json_decode(plates_info):
# Check whether plate was externally extracted
if ee is True:
# find the id of null things
eq_no = \
Equipment.list_equipment('Not applicable')[0]['equipment_id']
ep = ept = kf = Equipment(eq_no)
kit = ReagentComposition.from_external_id('Not applicable')
else:
kf = Equipment(kf)
ep = Equipment(ep)
ept = Equipment(ept)
kit = ReagentComposition.from_external_id(kit)
processes.append(
GDNAExtractionProcess.create(self.current_user,
Plate(pid),
kf,
ep,
ept,
kit,
volume,
p_name,
externally_extracted=ee,
extraction_date=extraction_date,
notes=nt).id)
self.write({'processes': processes})
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'))