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'])
# calculate estimated molar fraction for each element of pool
amts = plate_result['comp_vals'] * plate_result['pool_vals']
pcts = amts / amts.sum()
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 get(self):
pool_type = 'shotgun_plate'
plate_ids = self.get_arguments('plate_id')
process_id = self.get_argument('process_id', None)
input_plate = None
pool_func_data = None
pool_values = []
pool_blanks = []
plate_names = []
if process_id is not None:
try:
process = PoolingProcess(process_id)
except LabControlUnknownIdError:
raise HTTPError(404, reason="Pooling process %s doesn't exist"
% process_id)
plate = process.components[0][0].container.plate
input_plate = plate.id
pool_func_data = process.pooling_function_data
content_type = type(plate.get_well(1, 1).composition)
id_plate_type = PLATE_TYPES[content_type]
plate_type_mapped = PLATE_TYPE_TO_POOL_TYPE[id_plate_type]
if plate_type_mapped != pool_type:
raise HTTPError(400, reason='Pooling process type does not '
'match pooling type')
_, pool_values, pool_blanks, plate_names = \
make_2D_arrays(plate, process.quantification_process)
pool_values = pool_values.tolist()
pool_blanks = pool_blanks.tolist()
plate_names = plate_names.tolist()
elif len(plate_ids) > 0:
content_types = {type(Plate(pid).get_well(1, 1).composition)
for pid in plate_ids}
if len(content_types) > 1:
raise HTTPError(400, reason='Plates contain different types '
'of compositions')
# check if the observed plates are the same type as the pooling
# type (i.e., no shotgun plates for 16S pooling)
content_type = content_types.pop()
id_plate_type = PLATE_TYPES[content_type]
plate_type_mapped = PLATE_TYPE_TO_POOL_TYPE[id_plate_type]
if plate_type_mapped != pool_type:
raise HTTPError(400, reason='Plate type does not match '
'pooling type')
pool_type_stripped = POOL_TYPE_PARAMS[pool_type]['abbreviation']
plate_type = POOL_TYPE_TO_PLATE_TYPE[pool_type]
robots = (Equipment.list_equipment('EpMotion') +
Equipment.list_equipment('echo'))
template = POOL_TYPE_PARAMS[pool_type]['template']
self.render(template, plate_ids=plate_ids,
robots=robots, pool_params=HTML_POOL_PARAMS,
input_plate=input_plate, pool_func_data=pool_func_data,
process_id=process_id, pool_values=pool_values,
plate_type=plate_type, pool_blanks=pool_blanks,
plate_names=plate_names, pool_type=pool_type_stripped)
def test_list_equipment(self):
obs = Equipment.list_equipment()
exp = [{
'equipment_id': 15,
'external_id': '108379Z'
}, {
'equipment_id': 16,
'external_id': '109375A'
}, {
'equipment_id': 17,
'external_id': '311411B'
}, {
'equipment_id': 2,
'external_id': 'BUZZ'
}, {
'equipment_id': 10,
'external_id': 'Carmen'
}, {
'equipment_id': 1,
'external_id': 'Echo550'
}, {
'equipment_id': 9,
'external_id': 'HOWE'
}, {
'equipment_id': 19,
'external_id': 'IGM-HiSeq4000'
}, {
'equipment_id': 8,
'external_id': 'JER-E'
}, {
'equipment_id': 11,
'external_id': 'KF1'
}, {
'equipment_id': 12,
'external_id': 'KF2'
}, {
'equipment_id': 13,
'external_id': 'KF3'
}, {
'equipment_id': 14,
'external_id': 'KF4'
}, {
'equipment_id': 18,
'external_id': 'KL-MiSeq'
}, {
'equipment_id': 5,
'external_id': 'LUCY'
}, {
'equipment_id': 20,
'external_id': 'Not applicable'
}, {
'equipment_id': 4,
'external_id': 'PRICKLY'
}, {
'equipment_id': 7,
'external_id': 'RIK-E'
}, {
'equipment_id': 6,
'external_id': 'ROB-E'
}]
self.assertEqual(obs[:-1], exp)
obs = Equipment.list_equipment('echo')
exp = [{'equipment_id': 1, 'external_id': 'Echo550'}]
self.assertEqual(obs, exp)
obs = Equipment.list_equipment('mosquito')
exp = [{
'equipment_id': 2,
'external_id': 'BUZZ'
}, {
'equipment_id': 4,
'external_id': 'PRICKLY'
}, {
'equipment_id': 3,
'external_id': 'STINGER'
}]
self.assertEqual(obs, exp)
def post(self):
equipment_type = self.get_argument('equipment_type')
external_id = self.get_argument('external_id')
equipment = Equipment.create(equipment_type, external_id)
self.write({'equipment': equipment.id})
def get(self):
equipment_types = Equipment.list_equipment_types()
self.render('equipments.html', equipment_types=equipment_types)
def create_compression_process(user, gdna_plates):
comp_process = GDNAPlateCompressionProcess.create(
user, gdna_plates, 'Compressed test plate %s' % datetime.now(),
Equipment(6))
compressed_plate = comp_process.plates[0]
return comp_process, compressed_plate