def get(self, process_id):
process = LibraryPrepShotgunProcess(int(process_id))
text = process.generate_echo_picklist()
compressed_plate_name = process.normalization_process.compressed_plate\
.external_id
name_pieces = [compressed_plate_name, "indices"]
self.deliver_text(name_pieces, process, text)
def get(self, process_id):
process = LibraryPrepShotgunProcess(int(process_id))
text = process.generate_echo_picklist()
self.set_header('Content-Description', 'text/csv')
self.set_header('Expires', '0')
self.set_header('Cache-Control', 'no-cache')
self.set_header(
'Content-Disposition', 'attachment; filename='
'LibraryPrepShotgunSheet_%s.csv' % process_id)
self.write(text)
self.finish()
def get(self):
plate_ids = self.get_arguments('plate_id')
process_id = self.get_argument('process_id', None)
kappa = None
stub = None
volume = None
norm_plate = None
i5plate = None
i7plate = None
if process_id is not None:
try:
process = LibraryPrepShotgunProcess(process_id)
except LabmanUnknownIdError:
raise HTTPError(404,
reason="Shotgun library prep process %s "
"doesn't exist" % process_id)
kappa = process.kappa_hyper_plus_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 = Plate.list_plates(['primer'])
self.render('library_prep_shotgun.html',
plate_ids=plate_ids,
primer_plates=primer_plates,
process_id=process_id,
kappa=kappa,
stub=stub,
volume=volume,
norm_plate=norm_plate,
i5plate=i5plate,
i7plate=i7plate)
def create_shotgun_process(user, norm_plate):
kappa = ReagentComposition(4)
stub = ReagentComposition(5)
shotgun_process = LibraryPrepShotgunProcess.create(
user, norm_plate, 'Test Shotgun Library %s' % datetime.now(), kappa,
stub, 4000, Plate(19), Plate(20))
shotgun_plate = shotgun_process.plates[0]
return shotgun_process, shotgun_plate
def create_shotgun_process(user, norm_plate):
kappa = ReagentComposition(4)
stub = ReagentComposition(5)
primer_a, primer_b = get_primer_plate(is_96=False)
shotgun_process = LibraryPrepShotgunProcess.create(
user, norm_plate, 'Test Shotgun Library %s' % datetime.now(), kappa,
stub, 4000, primer_a, primer_b)
shotgun_plate = shotgun_process.plates[0]
return shotgun_process, shotgun_plate
def post(self):
plate_name = self.get_argument('plate_name')
volume = self.get_argument('volume')
plate = self.get_argument('plate')
i5_plate = self.get_argument('i5_plate')
i7_plate = self.get_argument('i7_plate')
kappa_hyper_plus_kit = self.get_argument('kappa_hyper_plus_kit')
stub_lot = self.get_argument('stub_lot')
process = LibraryPrepShotgunProcess.create(
self.current_user, Plate(plate), plate_name,
ReagentComposition.from_external_id(kappa_hyper_plus_kit),
ReagentComposition.from_external_id(stub_lot), volume,
Plate(i5_plate), Plate(i7_plate))
self.write({'process': process.id})
def post(self):
user = self.current_user
plates_info = self.get_argument('plates_info')
volume = self.get_argument('volume')
kappa_hyper_plus_kit = self.get_argument('kappa_hyper_plus_kit')
stub_lot = self.get_argument('stub_lot')
processes = [[
pid,
LibraryPrepShotgunProcess.create(
user, Plate(pid), plate_name,
ReagentComposition.from_external_id(kappa_hyper_plus_kit),
ReagentComposition.from_external_id(stub_lot), volume,
Plate(i5p), Plate(i7p)).id
] for pid, plate_name, i5p, i7p in json_decode(plates_info)]
self.write({'processes': processes})