def setUp(self):
self.experiment = Experiment(name='backgroundcolor',
state=ENABLED_STATE)
self.experiment.save()
self.request = request_factory.get('/',
HTTP_USER_AGENT='GoogleBot/2.1')
self.experiment_counter = ExperimentCounter()
def test_experiment_is_related_to_owner(self):
owner = User.objects.first()
experiment = Experiment(nes_id=17,
owner=owner,
version=1,
sent_date=datetime.utcnow())
experiment.save()
self.assertIn(experiment, owner.experiment_set.all())
def setUp(self):
self.experiment = Experiment(name='mock_experiment')
self.instance = AdminConditional(
description='mock template',
experiment=self.experiment,
)
self.request = mock.MagicMock()
self.context = {'request': self.request}
self.experiments = mock.MagicMock()
self.experiments.context = self.context
self.request.experiments = self.experiments
def test_duplicate_experiments_are_invalid(self):
owner = User.objects.first()
Experiment.objects.create(nes_id=17,
owner=owner,
version=1,
sent_date=datetime.utcnow())
experiment = Experiment(nes_id=17,
owner=owner,
version=1,
sent_date=datetime.utcnow())
with self.assertRaises(ValidationError):
experiment.full_clean()
def test_cannot_save_empty_attributes(self):
owner = User.objects.first()
# version=17: large number to avoid conflicts with global setup
experiment = Experiment(nes_id=1,
title='',
description='',
owner=owner,
version=17,
slug='',
sent_date=datetime.utcnow())
# TODO: slug='' does not raises ValidationError
with self.assertRaises(ValidationError):
experiment.save()
experiment.full_clean()
def test_default_attributes(self):
experiment = Experiment()
self.assertEqual(experiment.nes_id, None)
self.assertEqual(experiment.title, '')
self.assertEqual(experiment.description, '')
self.assertEqual(experiment.data_acquisition_done, False)
self.assertEqual(experiment.sent_date, None)
self.assertEqual(experiment.version, None)
self.assertEqual(experiment.status, experiment.RECEIVING)
self.assertEqual(experiment.trustee, None)
self.assertEqual(experiment.project_url, None)
self.assertEqual(experiment.ethics_committee_url, None)
self.assertEqual(experiment.ethics_committee_file, None)
self.assertEqual(experiment.slug, '')
self.assertEqual(experiment.downloads, 0)
def addexperiment(request, checksum):
dir_path = 'media/datasets/' + checksum + "/"
dump_file = dir_path + "dataset.csv"
meta_file = dir_path + "metadata.json"
if request.method == "POST":
auth = request.META['HTTP_AUTHORIZATION'].split()
username, password = base64.b64decode(
auth[1]).decode("utf-8").split(':')
user = authenticate(username=username, password=password)
if user is None or user.is_active == False:
return HttpResponse('AUTHENTICATION_FAILED')
if Experiment.objects.filter(checksum=checksum).exists():
return HttpResponse('DATASET_ALREADY_IN_DB')
with open(meta_file, "r") as f:
experiment_meta = json.load(f)
sensors_abbrs = list(pd.read_csv(dump_file, nrows=1).columns)
sensors_abbrs.remove('time')
sensors = {
sensor['abbreviation']: sensor['id']
for sensor in list(
Sensor.objects.filter(abbreviation__in=sensors_abbrs).values(
'abbreviation', 'id'))
}
with open(dump_file, "r") as f:
num_lines = sum(1 for line in f) - 1
experiment_start_unix = int(
time.mktime(
time.strptime(experiment_meta['start_time'],
'%Y-%m-%d %H:%M:%S'))) * (10**6)
rock = Rock.objects.get(id=experiment_meta['rock_id'])
experiment = Experiment(start_time=experiment_meta['start_time'],
description=experiment_meta['description'],
rock_id=rock,
checksum=checksum,
nr_data_points=num_lines * len(sensors_abbrs))
experiment.sensors = [id for id in sensors.values()]
experiment.save()
add_experiment_to_db.delay(checksum)
return HttpResponse('EXPERIMENT_BEING_ADDED_TO_THE_DB')
def handle(self, *args, **options):
try:
user_data = {}
if hasattr(self.stdin, 'isatty') and not self.stdin.isatty():
raise NotRunningInTTYException("Not running in a TTY")
for field_name in Experiment.REQUIRED_FIELDS:
field = Experiment._meta.get_field(field_name)
user_data[field_name] = None
while user_data[field_name] is None:
message = field_name.upper() + ': '
user_data[field_name] = self.get_input_data(field, message)
except KeyboardInterrupt:
self.stderr.write("\nOperation cancelled.")
sys.exit(1)
except NotRunningInTTYException:
self.stdout.write(
"Experiment creation skipped due to not running in a TTY. "
"You can run `manage.py create_exp` in your project "
"to create one manually.")
app_name = user_data['name']
if app_name not in settings.INSTALLED_APPS:
try:
src = 'exp0'
dest = app_name
shutil.copytree(src, dest)
except Exception as e:
self.stderr.write("Directory not copied. Error: %s" % str(e))
try:
template_dir = app_name + '/templates/' + app_name
os.makedirs(template_dir)
with open("vlab/settings.py", "a") as myFile:
myFile.write("INSTALLED_APPS += ('%s',)\n" % app_name)
myFile.close()
experiment = Experiment(**user_data)
experiment.save()
except Exception as e:
self.stderr.write("Directory not copied. Error 1: %s" % str(e))
shutil.rmtree(app_name)
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 test_can_save_same_experiment_to_different_owners(self):
owner1 = User.objects.get(username='******')
owner2 = User.objects.get(username='******')
Experiment.objects.create(
title='A title',
description='A description',
nes_id=1,
owner=owner1,
version=17,
sent_date=datetime.utcnow(),
slug='slug6' # last slug in tests_helper was 'slug'
)
experiment2 = Experiment(title='A title',
description='A description',
nes_id=1,
owner=owner2,
version=17,
sent_date=datetime.utcnow(),
slug='slug7')
experiment2.full_clean()
def setUp(self):
self.experiment = Experiment(name='backgroundcolor',
state=ENABLED_STATE)
self.experiment.save()
self.request = request_factory.get('/')
self.request.session = DatabaseSession()
def setUp(self):
self.experiment = Experiment(name=EXPERIMENT_NAME, state=ENABLED_STATE)
self.experiment.save()
self.request = request_factory.get('/')
self.request.session = DatabaseSession()
self.experiment_counter = ExperimentCounter()
def setUp(self):
self.experiment = Experiment(name='backgroundcolor',
state=ENABLED_STATE)
self.experiment.save()
self.experiment_counter = ExperimentCounter()
