def _compute_pools(self, plate_info):
super()._compute_pools(plate_info)
self.params['total_each'] = False
self.params['vol_constant'] = 10 ** 9
pool_vals = self.function(self.raw_concs, **self.params)
# if adjust blank volume, do that
if self.params['blank_vol'] != '':
bv = self.params['blank_vol']
pool_vals = PoolingProcess.adjust_blank_vols(pool_vals,
self.comp_blanks,
bv)
# if only pool some blanks, do that
if self.params['blank_num'] != '':
bn = int(self.params['blank_num'])
pool_vals = PoolingProcess.select_blanks(pool_vals,
self.raw_concs,
self.comp_blanks,
bn)
# estimate pool volume and concentration
cs = self.comp_concs
total_c, total_v = PoolingProcess.estimate_pool_conc_vol(pool_vals, cs)
# store output values
output = {}
output['func_data'] = {'function': self.func_name,
'parameters': self.params}
output['raw_vals'] = self.raw_concs
output['comp_vals'] = self.comp_concs
output['pool_vals'] = pool_vals
output['pool_blanks'] = self.comp_blanks.tolist()
output['plate_names'] = self.plate_names.tolist()
output['plate_id'] = self.plate_id
output['destination'] = self.params['destination']
output['robot'] = self.params['robot']
output['blank_vol'] = self.params['blank_vol']
output['blank_num'] = self.params['blank_num']
output['total_conc'] = total_c
output['total_vol'] = total_v
output['quant-process-id'] = self.quant_process_id
return output
def _compute_pools(self, plate_info):
super()._compute_pools(plate_info)
# pool_vals looks like its needed in the output
pool_vals = self.function(self.raw_concs, **self.params)
# if adjust blank volume, do that
if self.params['blank_vol'] != '':
pool_vals = PoolingProcess.adjust_blank_vols(
pool_vals, self.comp_blanks, self.params['blank_vol'])
# if only pool some blanks, do that
if self.params['blank_num'] != '':
pool_vals = PoolingProcess.select_blanks(
pool_vals, self.raw_concs, self.comp_blanks,
int(self.params['blank_num']))
# estimate pool volume and concentration
total_c, total_v = PoolingProcess.estimate_pool_conc_vol(
pool_vals, self.comp_concs)
# store output values
output = {}
output['pool_vals'] = pool_vals
output['pool_blanks'] = self.comp_blanks.tolist()
output['plate_names'] = self.plate_names.tolist()
output['plate_id'] = self.plate_id
output['destination'] = self.params['destination']
output['robot'] = self.params['robot']
output['blank_vol'] = self.params['blank_vol']
output['blank_num'] = self.params['blank_num']
output['total_conc'] = total_c
output['total_vol'] = total_v
output['quant-process-id'] = self.quant_process_id
return output
def _compute_pools(self, plate_info):
plate_id = plate_info['plate-id']
func_name = plate_info['pool-func']
plate_type = plate_info['plate-type']
quant_process_id = plate_info['quant-process-id']
func_info = POOL_FUNCS[func_name]
function = func_info['function']
plate = Plate(plate_id)
quant_process = QuantificationProcess(quant_process_id)
# make params dictionary for function
params = {}
for arg, pfx in func_info['parameters']:
param_key = '%s%s' % (pfx, plate_id)
if param_key not in plate_info:
raise HTTPError(
400, reason='Missing parameter %s' % param_key)
# empty strings are sent when we have disabled inputs.
# we are testing for them explicitly where expected.
if plate_info[param_key] != '':
params[arg] = float(plate_info[param_key])
else:
params[arg] = plate_info[param_key]
# compute molar concentrations
quant_process.compute_concentrations(size=params['size'])
# calculate pooled values
raw_concs, comp_concs, comp_blanks, \
plate_names = make_2D_arrays(plate, quant_process)
# for 16S, we calculate each sample independently
pool_type = PLATE_TYPE_TO_POOL_TYPE[plate_type]
params['total_each'] = POOL_TYPE_PARAMS[pool_type]['total_each']
params['vol_constant'] = POOL_TYPE_PARAMS[pool_type]['vol_constant']
pool_vals = function(raw_concs, **params)
# if adjust blank volume, do that
if params['blank_vol'] != '':
pool_vals = PoolingProcess.adjust_blank_vols(pool_vals,
comp_blanks,
params['blank_vol'])
# if only pool some blanks, do that
if params['blank_num'] != '':
pool_vals = PoolingProcess.select_blanks(pool_vals,
raw_concs,
comp_blanks,
int(params['blank_num']))
# estimate pool volume and concentration
total_c, total_v = PoolingProcess.estimate_pool_conc_vol(pool_vals,
comp_concs)
# store output values
output = {}
output['func_data'] = {'function': func_name,
'parameters': params}
output['raw_vals'] = raw_concs
output['comp_vals'] = comp_concs
output['pool_vals'] = pool_vals
output['pool_blanks'] = comp_blanks.tolist()
output['plate_names'] = plate_names.tolist()
output['plate_id'] = plate_id
output['destination'] = params['destination']
output['robot'] = params['robot']
output['blank_vol'] = params['blank_vol']
output['blank_num'] = params['blank_num']
output['total_conc'] = total_c
output['total_vol'] = total_v
output['quant-process-id'] = quant_process_id
return output