def get_primer_plate(is_96):
plates = [
Plate(item['plate_id']) for item in Plate.list_plates(['primer'])
]
if is_96:
# use different plates for 16S
shuffle(plates)
hit = None
for plate in plates:
pc = plate.plate_configuration
if pc.description == '96-well microtiter plate':
hit = plate
break
if hit is None:
raise ValueError("Unable to identify a primer plate")
return (hit, None)
else:
# not shuffling as the order of the plates implicitly matters
hits = []
for plate in plates:
pc = plate.plate_configuration
if pc.description == '384-well microtiter plate':
if 'primer' in plate.external_id.lower():
hits.append(plate)
hits = hits[:2]
if len(hits) != 2:
raise ValueError("Unable to identify two primer plates")
return hits
def test_plate_list_include_timestamp(self):
# ...limit pathological failures by testing within an hour of creation
exp = datetime.datetime.now()
exp = str(datetime.datetime(exp.year, exp.month,
exp.day)).split(None, 1)[0]
for i in Plate.list_plates():
obs = i['creation_timestamp'].split(None, 1)[0]
self.assertEqual(obs, exp)
def get(self):
plate_ids = self.get_arguments('plate_id')
process_id = self.get_argument('process_id', None)
gdna_plate = None
epmotion = None
epmotion_tm300 = None
epmotion_tm50 = None
primer_plate = None
master_mix = None
water_lot = None
volume = None
prep_date = None
if process_id is not None:
try:
process = LibraryPrep16SProcess(process_id)
except LabControlUnknownIdError:
raise HTTPError(404,
reason="Amplicon process %s doesn't exist" %
process_id)
gdna_plate = process.gdna_plate.id
epmotion = process.epmotion.id
epmotion_tm300 = process.epmotion_tm300_tool.id
epmotion_tm50 = process.epmotion_tm50_tool.id
master_mix = process.mastermix.external_lot_id
water_lot = process.water_lot.external_lot_id
primer_plate = process.primer_plate.id
volume = process.volume
prep_date = process.date.strftime(process.get_date_format())
robots = Equipment.list_equipment('EpMotion')
tools_tm300_8 = Equipment.list_equipment(
'tm 300 8 channel pipette head')
tools_tm50_8 = Equipment.list_equipment('tm 50 8 channel pipette head')
primer_plates = []
for pp in Plate.list_plates(['primer']):
plate = Plate(pp['plate_id'])
if plate.process.primer_set.target_name == 'Amplicon':
primer_plates.append(pp)
self.render('library_prep_16S.html',
plate_ids=plate_ids,
robots=robots,
tools_tm300_8=tools_tm300_8,
tools_tm50_8=tools_tm50_8,
primer_plates=primer_plates,
process_id=process_id,
gdna_plate=gdna_plate,
epmotion=epmotion,
epmotion_tm300=epmotion_tm300,
epmotion_tm50=epmotion_tm50,
master_mix=master_mix,
water_lot=water_lot,
primer_plate=primer_plate,
preparationDate=prep_date,
volume=volume)
def get(self):
plate_type = self.get_argument('plate_type', None)
only_quantified = self.get_argument('only_quantified', False)
plate_type = (json_decode(plate_type)
if plate_type is not None else None)
only_quantified = True if only_quantified == 'true' else False
rows_list = [[
p['plate_id'], p['external_id'], p['creation_timestamp'],
p['studies'] if p['studies'] is not None else []
] for p in Plate.list_plates(plate_type,
only_quantified=only_quantified,
include_study_titles=True)]
res = {"data": rows_list}
self.write(res)
def get(self):
plate_ids = self.get_arguments('plate_id')
process_id = self.get_argument('process_id', None)
kapa = None
stub = None
volume = None
norm_plate = None
i5plate = None
i7plate = None
if process_id is not None:
try:
process = LibraryPrepShotgunProcess(process_id)
except LabControlUnknownIdError:
raise HTTPError(404,
reason="Shotgun library prep process %s "
"doesn't exist" % process_id)
kapa = process.kapa_hyperplus_kit.external_lot_id
stub = process.stub_lot.external_lot_id
norm_plate = process.normalized_plate.id
i5plate = process.i5_primer_plate.id
i7plate = process.i7_primer_plate.id
volume = process.volume
primer_plates = []
for pp in Plate.list_plates(['primer']):
plate = Plate(pp['plate_id'])
if plate.process.primer_set.target_name == 'Shotgun':
primer_plates.append(pp)
self.render('library_prep_shotgun.html',
plate_ids=plate_ids,
primer_plates=primer_plates,
process_id=process_id,
kapa=kapa,
stub=stub,
volume=volume,
norm_plate=norm_plate,
i5plate=i5plate,
i7plate=i7plate)
def test_plate_list_discarded_functionality(self):
# test case based on the test_list_plates
obs = self.strip_out_creation_timestamp(Plate.list_plates())
Plate(21).discard = True
self.assertGreaterEqual(len(obs), 25)
self.assertEqual(obs[0], {
'plate_id': 1,
'external_id': 'EMP 16S V4 primer plate 1'
})
self.assertEqual(obs[16], {
'plate_id': 17,
'external_id': 'EMP 16S V4 primer plate 7 10/23/2017'
})
self.assertEqual(obs[20], {
'plate_id': 21,
'external_id': 'Test plate 1'
})
Plate(21).discard = False
# Test without returning discarded primer plates
Plate(11).discarded = True
Plate(12).discarded = True
Plate(13).discarded = True
obs = self.strip_out_creation_timestamp(
Plate.list_plates(['primer'], include_discarded=False))
exp = [{
'plate_id': 14,
'external_id': 'EMP 16S V4 primer plate 4 10/23/2017'
}, {
'plate_id': 15,
'external_id': 'EMP 16S V4 primer plate 5 10/23/2017'
}, {
'plate_id': 16,
'external_id': 'EMP 16S V4 primer plate 6 10/23/2017'
}, {
'plate_id': 17,
'external_id': 'EMP 16S V4 primer plate 7 10/23/2017'
}, {
'plate_id': 18,
'external_id': 'EMP 16S V4 primer plate 8 10/23/2017'
}, {
'plate_id': 19,
'external_id': 'iTru 5 Primer Plate 10/23/2017'
}, {
'plate_id': 20,
'external_id': 'iTru 7 Primer Plate 10/23/2017'
}]
self.assertEqual(obs, exp)
# Test returning discarded primer plates
obs = self.strip_out_creation_timestamp(
Plate.list_plates(['primer'], include_discarded=True))
exp = [{
'plate_id': 11,
'external_id': 'EMP 16S V4 primer plate 1 10/23/2017'
}, {
'plate_id': 12,
'external_id': 'EMP 16S V4 primer plate 2 10/23/2017'
}, {
'plate_id': 13,
'external_id': 'EMP 16S V4 primer plate 3 10/23/2017'
}, {
'plate_id': 14,
'external_id': 'EMP 16S V4 primer plate 4 10/23/2017'
}, {
'plate_id': 15,
'external_id': 'EMP 16S V4 primer plate 5 10/23/2017'
}, {
'plate_id': 16,
'external_id': 'EMP 16S V4 primer plate 6 10/23/2017'
}, {
'plate_id': 17,
'external_id': 'EMP 16S V4 primer plate 7 10/23/2017'
}, {
'plate_id': 18,
'external_id': 'EMP 16S V4 primer plate 8 10/23/2017'
}, {
'plate_id': 19,
'external_id': 'iTru 5 Primer Plate 10/23/2017'
}, {
'plate_id': 20,
'external_id': 'iTru 7 Primer Plate 10/23/2017'
}]
self.assertEqual(obs, exp)
# undo the discarding
Plate(11).discarded = False
Plate(12).discarded = False
Plate(13).discarded = False
def test_list_plates(self):
# Test returning all plates
obs = self.strip_out_creation_timestamp(Plate.list_plates())
# We are creating plates below, but at least we know there are 35
# plates in the test database
self.assertGreaterEqual(len(obs), 35)
self.assertEqual(obs[0], {
'plate_id': 1,
'external_id': 'EMP 16S V4 primer plate 1'
})
self.assertEqual(obs[16], {
'plate_id': 17,
'external_id': 'EMP 16S V4 primer plate 7 10/23/2017'
})
self.assertEqual(obs[20], {
'plate_id': 21,
'external_id': 'Test plate 1'
})
# Test returning sample plates
obs = self.strip_out_creation_timestamp(Plate.list_plates(['sample']))
self.assertGreaterEqual(len(obs), 4)
self.assertEqual(obs[0], {
'plate_id': 21,
'external_id': 'Test plate 1'
})
obs = self.strip_out_creation_timestamp(
Plate.list_plates(['sample'], include_study_titles=True))
self.assertGreaterEqual(len(obs), 4)
self.assertEqual(
obs[0], {
'plate_id':
21,
'external_id':
'Test plate 1',
'studies':
['Identification of the Microbiomes '
'for Cannabis Soils']
})
# Test returning gDNA plates
obs = self.strip_out_creation_timestamp(Plate.list_plates(['gDNA']))
self.assertEqual(obs, [{
'plate_id': 22,
'external_id': 'Test gDNA plate 1'
}, {
'external_id': 'Test gDNA plate 2',
'plate_id': 28
}, {
'external_id': 'Test gDNA plate 3',
'plate_id': 31
}, {
'external_id': 'Test gDNA plate 4',
'plate_id': 34
}])
obs = self.strip_out_creation_timestamp(
Plate.list_plates(['compressed gDNA']))
self.assertEqual(obs, [{
'plate_id': 24,
'external_id': 'Test compressed gDNA plates 1-4'
}])
# Test returning primer plates
obs = self.strip_out_creation_timestamp(Plate.list_plates(['primer']))
exp = [{
'plate_id': 11,
'external_id': 'EMP 16S V4 primer plate 1 10/23/2017'
}, {
'plate_id': 12,
'external_id': 'EMP 16S V4 primer plate 2 10/23/2017'
}, {
'plate_id': 13,
'external_id': 'EMP 16S V4 primer plate 3 10/23/2017'
}, {
'plate_id': 14,
'external_id': 'EMP 16S V4 primer plate 4 10/23/2017'
}, {
'plate_id': 15,
'external_id': 'EMP 16S V4 primer plate 5 10/23/2017'
}, {
'plate_id': 16,
'external_id': 'EMP 16S V4 primer plate 6 10/23/2017'
}, {
'plate_id': 17,
'external_id': 'EMP 16S V4 primer plate 7 10/23/2017'
}, {
'plate_id': 18,
'external_id': 'EMP 16S V4 primer plate 8 10/23/2017'
}, {
'plate_id': 19,
'external_id': 'iTru 5 Primer Plate 10/23/2017'
}, {
'plate_id': 20,
'external_id': 'iTru 7 Primer Plate 10/23/2017'
}]
self.assertEqual(obs, exp)
# Test returning gDNA and compressed gDNA plates
obs = self.strip_out_creation_timestamp(
Plate.list_plates(['gDNA', 'compressed gDNA']))
self.assertEqual(obs, [{
'plate_id': 22,
'external_id': 'Test gDNA plate 1'
}, {
'plate_id': 24,
'external_id': 'Test compressed gDNA plates 1-4'
}, {
'external_id': 'Test gDNA plate 2',
'plate_id': 28
}, {
'external_id': 'Test gDNA plate 3',
'plate_id': 31
}, {
'external_id': 'Test gDNA plate 4',
'plate_id': 34
}])
obs = self.strip_out_creation_timestamp(
Plate.list_plates(['compressed gDNA', 'normalized gDNA']))
self.assertEqual(obs, [{
'plate_id': 24,
'external_id': 'Test compressed gDNA plates 1-4'
}, {
'plate_id': 25,
'external_id': 'Test normalized gDNA plates 1-4'
}])
obs = self.strip_out_creation_timestamp(
Plate.list_plates(['compressed gDNA', 'normalized gDNA'],
only_quantified=True,
include_study_titles=True))
self.assertEqual(obs, [{
'plate_id':
24,
'external_id':
'Test compressed gDNA plates 1-4',
'studies':
['Identification of the Microbiomes '
'for Cannabis Soils']
}])