def post(self):
pool_name = self.get_argument('pool_name')
pools_info = json_decode(self.get_argument('pools_info'))
concentrations = []
input_compositions = []
for p_info in pools_info:
pool_comp = PoolComposition(p_info['pool_id'])
concentrations.append({
'composition': pool_comp,
'concentration': p_info['concentration']
})
input_compositions.append({
'composition':
pool_comp,
'input_volume':
p_info['volume'],
'percentage_of_output':
p_info['percentage']
})
# Create the quantification process (DNA conc)
q_process = QuantificationProcess.create_manual(
self.current_user, concentrations)
# Create the pool - Magic number 5 - > the volume for this poolings
# is always 5 according to the wet lab.
p_process = PoolingProcess.create(self.current_user, q_process,
pool_name, 5, input_compositions, {
"function": "amplicon_pool",
"parameters": {}
})
self.write({'process': p_process.id})
def post(self):
plates_info = json_decode(self.get_argument('plates-info'))
results = []
for pinfo in plates_info:
plate_result = self._compute_pools(pinfo)
plate = Plate(plate_result['plate_id'])
pool_name = 'Pool from plate %s (%s)' % (
plate.external_id,
datetime.now().strftime('%Y-%m-%d %H:%M:%S'))
# create input molar percentages
pcts = calc_pool_pcts(plate_result['comp_vals'],
plate_result['pool_vals'])
quant_process = plate.quantification_process
input_compositions = []
for comp, _, _ in quant_process.concentrations:
well = comp.container
row = well.row - 1
column = well.column - 1
input_compositions.append(
{'composition': comp,
'input_volume': plate_result['pool_vals'][row][column],
'percentage_of_output': pcts[row][column]})
robot = (Equipment(plate_result['robot'])
if plate_result['robot'] is not None else None)
process = PoolingProcess.create(
self.current_user, quant_process, pool_name,
plate_result['pool_vals'].sum(), input_compositions,
plate_result['func_data'], robot=robot,
destination=plate_result['destination'])
results.append({'plate-id': plate.id, 'process-id': process.id})
self.write(json_encode(results))
def post(self):
plate_id = self.get_argument('plate-id')
concentrations = json_decode(self.get_argument('concentrations'))
concentrations = np.asarray(concentrations)
plate = Plate(plate_id)
q_process = QuantificationProcess.create(self.current_user, plate,
concentrations)
pool_name = 'Pool - %s' % plate.external_id
input_compositions = []
concentrations = q_process.concentrations
total_vol = 0
for conc in concentrations:
in_vol = conc[1]
total_vol += in_vol
input_compositions.append({
'composition': conc[0],
'input_volume': in_vol,
'percentage_of_output': in_vol
})
for ic in input_compositions:
ic['percentage_of_output'] = ic['percentage_of_output'] / total_vol
process = PoolingProcess.create(self.current_user, q_process,
pool_name, total_vol,
input_compositions)
self.write({'process': process.id})
def create_pools_pool_process(user, quant_process, pools):
input_compositions = [
{'composition': p, 'input_volume': 1, 'percentage_of_output': 1/9.0}
for p in pools]
pool_process = PoolingProcess.create(
user, quant_process, 'New pool name %s' % datetime.now(), 5,
input_compositions, {"function": "amplicon_pool", "parameters": {}})
return pool_process
def create_plate_pool_process(user, quant_process, plate, func_data):
input_compositions = []
echo = Equipment(8)
for well in chain.from_iterable(plate.layout):
if well is not None:
input_compositions.append({
'composition': well.composition, 'input_volume': 1,
'percentage_of_output': 1/9.0})
pool_process = PoolingProcess.create(
user, quant_process, 'New test pool name %s' % datetime.now(),
4, input_compositions, func_data, robot=echo)
return pool_process