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'])
# create input molar percentages
pcts = calc_pool_pcts(plate_result['comp_vals'],
plate_result['pool_vals'])
quant_process = QuantificationProcess(
plate_result['quant-process-id'])
pool_name = 'Pool from plate %s (%s)' % (
plate.external_id,
datetime.now().strftime(quant_process.get_date_format()))
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 create_pool_quantification_process(user, pools):
concentrations = np.around(np.random.rand(len(pools)), 6)
concentrations = [{
'composition': p,
'concentration': c
} for p, c in zip(pools, concentrations)]
return QuantificationProcess.create_manual(user, concentrations)
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):
user = self.current_user
plates_info = self.get_argument('plates_info')
water = self.get_argument('water')
total_vol = self.get_argument('total_vol')
ng = self.get_argument('ng')
min_vol = self.get_argument('min_vol')
max_vol = self.get_argument('max_vol')
resolution = self.get_argument('resolution')
reformat = self.get_argument('reformat')
processes = [[
plate_id,
NormalizationProcess.create(
user,
QuantificationProcess(quantification_process_id),
ReagentComposition.from_external_id(water),
plate_name,
total_vol=float(total_vol),
ng=float(ng),
min_vol=float(min_vol),
max_vol=float(max_vol),
resolution=float(resolution),
reformat=reformat).id
] for plate_id, plate_name, quantification_process_id in json_decode(
plates_info)]
self.write({'processes': processes})
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 post(self):
# We will receive as many files as plates the user has selected
# The key of the self.request.files dictionary is of the form
# plate-file-<PLATE_ID> so use the keys to know the plates
# that we need to quantify
plates = []
for key in self.request.files:
plate_id = key.rsplit('-', 1)[1]
# The 0 is because for each key we have a single file
file_content = self.request.files[key][0]['body'].decode('utf-8')
plate = Plate(plate_id)
pc = plate.plate_configuration
concentrations = QuantificationProcess.parse(file_content,
rows=pc.num_rows,
cols=pc.num_columns)
names = np.empty_like(plate.layout, dtype='object')
blanks = np.zeros_like(plate.layout, dtype=bool)
# fetch the sample names and whether or not the samples are blanks
# by default these are set to be None and False.
for i, full_row in enumerate(plate.layout):
for j, well in enumerate(full_row):
# some wells have no compositions at all so skip those
if well is None:
continue
comp = well.composition
# cache the sample compositions to avoid extra intermediate
# queries
if isinstance(comp, GDNAComposition):
smp = comp.sample_composition
elif isinstance(comp, (CompressedGDNAComposition,
LibraryPrep16SComposition)):
smp = comp.gdna_composition.sample_composition
elif isinstance(comp, LibraryPrepShotgunComposition):
smp = comp.normalized_gdna_composition\
.compressed_gdna_composition.gdna_composition\
.sample_composition
else:
raise ValueError('This composition type is not '
'supported')
blanks[i][j] = smp.sample_composition_type == 'blank'
names[i][j] = smp.sample_id
plates.append({
'plate_name': plate.external_id,
'plate_id': plate_id,
'concentrations': concentrations.tolist(),
'names': names.tolist(),
'blanks': blanks.tolist(),
'type': plate.process._process_type
})
self.render('quantification.html', plates=plates)
def post(self):
plates_info = json_decode(self.get_argument('plates-info'))
processes = []
for pinfo in plates_info:
plate = Plate(pinfo['plate_id'])
concentrations = np.asarray(pinfo['concentrations'])
processes.append(QuantificationProcess.create(
self.current_user, plate, concentrations).id)
self.write({'processes': processes})
def post(self):
plate_id = self.get_argument('plate-select')
# Magic number 0 -> there is only 1 file attached
file_content = self.request.files['plate-reader-fp'][0]['body'].decode(
'utf-8')
concentrations = QuantificationProcess.parse(file_content)
plate = Plate(plate_id)
self.render('quantification.html',
concentrations=concentrations.tolist(),
plate_name=plate.external_id,
plate_id=plate.id,
plate_conf=plate.plate_configuration.description)
def post(self):
# We will receive as many files as plates the user has selected
# The key of the self.request.files dictionary is of the form
# plate-file-<PLATE_ID> so use the keys to know the plates
# that we need to quantify
plates = []
for key in self.request.files:
plate_id = key.rsplit('-', 1)[1]
# The 0 is because for each key we have a single file
file_content = self.request.files[key][0]['body'].decode('utf-8')
plate = Plate(plate_id)
pc = plate.plate_configuration
concentrations = QuantificationProcess.parse(
file_content, rows=pc.num_rows, cols=pc.num_columns)
plates.append({'plate_name': plate.external_id,
'plate_id': plate_id,
'concentrations': concentrations.tolist()})
self.render('quantification.html', plates=plates)
def create_quantification_process(user, plate):
plate_config = plate.plate_configuration
concentrations = np.around(
np.random.rand(plate_config.num_rows, plate_config.num_columns), 6)
quant_process = QuantificationProcess.create(user, plate, concentrations)
return quant_process
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'))
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)
if plate_type == '16S library prep':
# for 16S, we calculate each sample independently
params['total_each'] = True
# constant accounts for both concentrations (ng/uL) and volumes
# (uL) in the same unit
params['vol_constant'] = 1
pool_vals = function(raw_concs, **params)
if plate_type == 'shotgun library prep':
# for shotgun, we calculate to a target total pool size
params['total_each'] = False
# constant handles volumes in nanoliters and concentrations in
# molarity (mol / L)
params['vol_constant'] = 10 ** 9
pool_vals = function(comp_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