def get(self):
plate_ids = self.get_arguments('plate_id')
process_id = self.get_argument('process_id', None)
gdna_plate = None
epmotion = None
epmotion_tm300 = None
epmotion_tm50 = None
primer_plate = None
master_mix = None
water_lot = None
volume = None
prep_date = None
if process_id is not None:
try:
process = LibraryPrep16SProcess(process_id)
except LabControlUnknownIdError:
raise HTTPError(404,
reason="Amplicon process %s doesn't exist" %
process_id)
gdna_plate = process.gdna_plate.id
epmotion = process.epmotion.id
epmotion_tm300 = process.epmotion_tm300_tool.id
epmotion_tm50 = process.epmotion_tm50_tool.id
master_mix = process.mastermix.external_lot_id
water_lot = process.water_lot.external_lot_id
primer_plate = process.primer_plate.id
volume = process.volume
prep_date = process.date.strftime(process.get_date_format())
robots = Equipment.list_equipment('EpMotion')
tools_tm300_8 = Equipment.list_equipment(
'tm 300 8 channel pipette head')
tools_tm50_8 = Equipment.list_equipment('tm 50 8 channel pipette head')
primer_plates = []
for pp in Plate.list_plates(['primer']):
plate = Plate(pp['plate_id'])
if plate.process.primer_set.target_name == 'Amplicon':
primer_plates.append(pp)
self.render('library_prep_16S.html',
plate_ids=plate_ids,
robots=robots,
tools_tm300_8=tools_tm300_8,
tools_tm50_8=tools_tm50_8,
primer_plates=primer_plates,
process_id=process_id,
gdna_plate=gdna_plate,
epmotion=epmotion,
epmotion_tm300=epmotion_tm300,
epmotion_tm50=epmotion_tm50,
master_mix=master_mix,
water_lot=water_lot,
primer_plate=primer_plate,
preparationDate=prep_date,
volume=volume)
def get(self):
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 = []
plate_type = None
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
_, 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')
plate_type = ('16S library prep'
if content_types.pop() == LibraryPrep16SComposition
else 'shotgun library prep')
robots = (Equipment.list_equipment('EpMotion') +
Equipment.list_equipment('echo'))
self.render('library_pooling.html',
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)
def get(self):
plate_ids = self.get_arguments('plate_id')
process_id = self.get_argument('process_id', None)
kingfisher = None
epmotion = None
epmotion_tool = None
extraction_kit = None
sample_plate = None
externally_extracted = False
volume = None
ext_date = None
notes = None
if process_id is not None:
try:
process = GDNAExtractionProcess(process_id)
except LabControlUnknownIdError:
raise HTTPError(404,
reason="Extraction process %s doesn't exist" %
process_id)
kingfisher = process.kingfisher.id
epmotion = process.epmotion.id
epmotion_tool = process.epmotion_tool.id
extraction_kit = process.extraction_kit.external_lot_id
sample_plate = process.sample_plate.id
externally_extracted = process.externally_extracted
volume = process.volume
ext_date = process.date.strftime(process.get_date_format())
notes = process.notes
ep_robots = Equipment.list_equipment('EpMotion')
kf_robots = Equipment.list_equipment('King Fisher')
tools = Equipment.list_equipment('tm 1000 8 channel pipette head')
self.render('extraction.html',
plate_ids=plate_ids,
kf_robots=kf_robots,
ep_robots=ep_robots,
tools=tools,
process_id=process_id,
kingfisher=kingfisher,
epmotion=epmotion,
epmotion_tool=epmotion_tool,
extraction_kit=extraction_kit,
sample_plate=sample_plate,
externally_extracted=externally_extracted,
volume=volume,
extraction_date=ext_date,
notes=notes)
def get(self, allowed_pools_type):
sequencers = []
allowed_pools_name = allowed_pools_type.split("_")[0].title()
for model, lanes in SequencingProcess.sequencer_lanes.items():
for sequencer in Equipment.list_equipment(model):
sequencer['lanes'] = lanes
sequencers.append(sequencer)
self.render('sequencing.html',
users=User.list_users(),
sequencers=sequencers,
allowed_pools_type=allowed_pools_type,
allowed_pools_name=allowed_pools_name)
def post(self):
plates_info = self.get_argument('plates_info')
extraction_date = self.get_argument('extraction_date')
volume = self.get_argument('volume')
month, day, year = map(int, extraction_date.split('/'))
extraction_date = date(year, month, day)
# We create one process per plate
processes = []
for pid, ee, kf, ep, ept, kit, p_name, nt in json_decode(plates_info):
# Check whether plate was externally extracted
if ee is True:
# find the id of null things
eq_no = \
Equipment.list_equipment('Not applicable')[0]['equipment_id']
ep = ept = kf = Equipment(eq_no)
kit = ReagentComposition.from_external_id('Not applicable')
else:
kf = Equipment(kf)
ep = Equipment(ep)
ept = Equipment(ept)
kit = ReagentComposition.from_external_id(kit)
processes.append(
GDNAExtractionProcess.create(self.current_user,
Plate(pid),
kf,
ep,
ept,
kit,
volume,
p_name,
externally_extracted=ee,
extraction_date=extraction_date,
notes=nt).id)
self.write({'processes': processes})
def get(self):
plate_ids = self.get_arguments('plate_id')
process_id = self.get_argument('process_id', None)
plate_name = None
robot = None
gdna_plates = []
if process_id is not None:
try:
process = GDNAPlateCompressionProcess(process_id)
except LabControlUnknownIdError:
raise HTTPError(404,
reason="Compression process %s doesn't "
"exist" % process_id)
plate_name = process.plates[0].external_id
robot = process.robot.id
gdna_plates = [p.id for p in process.gdna_plates]
robots = Equipment.list_equipment('EpMotion')
self.render('compression.html',
plate_ids=plate_ids,
robots=robots,
plate_name=plate_name,
robot=robot,
gdna_plates=gdna_plates,
process_id=process_id)
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)