def add_experiment_plate(request):
"""
Render the page to add a new experiment plate.
Adding an experiment plate also adds the corresponding experiment wells.
"""
if request.POST:
form = AddExperimentPlateForm(request.POST)
if form.is_valid():
data = form.cleaned_data
experiment_plate_id = data['experiment_plate_id']
ExperimentPlate.create_plate_and_wells(
experiment_plate_id, data['screen_stage'], data['date'],
data['temperature'], data['worm_strain'],
data['library_plate'], is_junk=data['is_junk'],
plate_comment=data['plate_comment'])
return redirect('experiment_plate_url', experiment_plate_id)
else:
form = AddExperimentPlateForm()
context = {
'form': form,
}
return render(request, 'add_experiment_plate.html', context)
def add_experiment_plate(request):
"""
Render the page to add a new experiment plate.
Adding an experiment plate also adds the corresponding experiment wells.
"""
if request.POST:
form = AddExperimentPlateForm(request.POST)
if form.is_valid():
data = form.cleaned_data
experiment_plate_id = data['experiment_plate_id']
ExperimentPlate.create_plate_and_wells(
experiment_plate_id,
data['screen_stage'],
data['date'],
data['temperature'],
data['worm_strain'],
data['library_plate'],
is_junk=data['is_junk'],
plate_comment=data['plate_comment'])
return redirect('experiment_plate_url', experiment_plate_id)
else:
form = AddExperimentPlateForm()
context = {
'form': form,
}
return render(request, 'add_experiment_plate.html', context)
def sync_experiment_row(legacy_row):
experiment_plate_id = legacy_row[0]
worm_strain = get_worm_strain(legacy_row[1], legacy_row[2])
legacy_library_plate_name = legacy_row[3]
temperature = legacy_row[4]
date = legacy_row[5]
is_junk = legacy_row[6]
comment = legacy_row[7]
all_match = True
if experiment_plate_id < 40000:
screen_stage = 1
else:
screen_stage = 2
new_plate = ExperimentPlate(id=experiment_plate_id,
screen_stage=screen_stage,
temperature=temperature,
date=date,
comment=comment)
all_match &= update_or_save_object(command, new_plate, recorded_plates,
plate_fields_to_compare)
experiment_plate = get_experiment_plate(experiment_plate_id)
for well in get_well_list():
new_well = Experiment(
id=generate_experiment_id(experiment_plate_id, well),
plate=experiment_plate,
well=well,
worm_strain=worm_strain,
library_stock=get_library_stock(legacy_library_plate_name,
well),
is_junk=is_junk)
all_match &= update_or_save_object(command, new_well,
recorded_wells,
well_fields_to_compare)
return all_match
def _parse_gdoc_experiment_rows(rows, screen_stage, date, worms,
temperatures):
"""Parse the rows with new experiments."""
all_new_plates = []
all_new_wells = []
for i, row in enumerate(rows):
current_row_number = FIRST_EXP_ROW + i + 1 # gdoc 1-indexed
library_plate_name = generate_library_plate_name(row[0])
if not library_plate_name:
raise ValueError('Library plate cannot be blank; see row {}'
.format(current_row_number))
try:
library_plate = LibraryPlate.objects.get(id=library_plate_name)
except ObjectDoesNotExist:
raise ValueError('Library Plate {} does not exist; see row {}'
.format(library_plate_name,
current_row_number))
for j, experiment_plate_id in enumerate(row[1:]):
if not experiment_plate_id:
continue
# Do dry_run=True to save inserts for bulk queries at end
plate, wells = ExperimentPlate.create_plate_and_wells(
experiment_plate_id, screen_stage, date,
temperatures[j], worms[j], library_plate, dry_run=True)
all_new_plates.append(plate)
all_new_wells.extend(wells)
ExperimentPlate.objects.bulk_create(all_new_plates)
Experiment.objects.bulk_create(all_new_wells)
return len(all_new_plates)
def __init__(self, **kwargs):
temperatures = ExperimentPlate.get_tested_temperatures()
kwargs["choices"] = [EMPTY_CHOICE] + [(x, x) for x in temperatures]
super(TemperatureChoiceField, self).__init__(**kwargs)
