def handle(self, **options):
require_db_write_acknowledgement()
return
if options['all']:
experiments = Experiment.objects.all()
else:
null_devstar_experiment_pks = (DevstarScore.objects.filter(
area_adult__isnull=True,
area_larva__isnull=True,
area_embryo__isnull=True).values_list('experiment', flat=True))
null_devstar_experiments = Experiment.objects.filter(
pk__in=null_devstar_experiment_pks)
all_devstar_experiment_pks = (
DevstarScore.objects.all().values_list('experiment',
flat=True))
no_devstar_experiments = Experiment.objects.exclude(
pk__in=all_devstar_experiment_pks)
experiments = sorted(chain(null_devstar_experiments,
no_devstar_experiments),
key=lambda instance: instance.id)
for experiment in experiments:
path = experiment.get_devstar_count_path()
if not os.path.isfile(path):
self.stderr.write('WARNING: Skipping experiment {} due to '
'DevStaR file not found'.format(experiment))
continue
counts = [None] * 6
with open(path, 'r') as f:
for line in f:
for i, pattern in enumerate(PATTERNS):
if line.startswith(pattern):
try:
counts[i] = int(line.split()[1])
except Exception:
raise CommandError('Error parsing line {} '
'in experiment {}'.format(
i, experiment))
for i, count in enumerate(counts):
if count is None:
self.stderr.write('WARNING: {} count is missing '
'for experiment {}'.format(
PATTERNS[i], experiment))
new_score = DevstarScore(
experiment=experiment,
is_bacteria_present=counts[0],
area_adult=counts[1],
area_larva=counts[2],
area_embryo=counts[3],
count_adult=counts[4],
count_larva=counts[5],
)
# If score already exists in database, check for match
try:
previous_score = DevstarScore.objects.get(
experiment=experiment)
if not previous_score.matches_raw_fields(new_score):
raise CommandError(
'The DevStaR txt output does '
'not match the existing database '
'entry for Experiment {}'.format(experiment))
except ObjectDoesNotExist:
self.stderr.write('DevStaR object not found for {}. '
'Attempting to save.'.format(experiment))
try:
new_score.full_clean()
except ValidationError:
raise CommandError(
'Cleaning DevStaR object {} '
'raised ValidationError'.format(new_score))
def handle(self, **options):
require_db_write_acknowledgement()
return
if options['all']:
experiments = Experiment.objects.all()
else:
null_devstar_experiment_pks = (
DevstarScore.objects.filter(
area_adult__isnull=True,
area_larva__isnull=True,
area_embryo__isnull=True)
.values_list('experiment', flat=True))
null_devstar_experiments = Experiment.objects.filter(
pk__in=null_devstar_experiment_pks)
all_devstar_experiment_pks = (
DevstarScore.objects.all()
.values_list('experiment', flat=True))
no_devstar_experiments = Experiment.objects.exclude(
pk__in=all_devstar_experiment_pks)
experiments = sorted(
chain(null_devstar_experiments, no_devstar_experiments),
key=lambda instance: instance.id)
for experiment in experiments:
path = experiment.get_devstar_count_path()
if not os.path.isfile(path):
self.stderr.write('WARNING: Skipping experiment {} due to '
'DevStaR file not found'
.format(experiment))
continue
counts = [None] * 6
with open(path, 'r') as f:
for line in f:
for i, pattern in enumerate(PATTERNS):
if line.startswith(pattern):
try:
counts[i] = int(line.split()[1])
except Exception:
raise CommandError('Error parsing line {} '
'in experiment {}'
.format(i, experiment))
for i, count in enumerate(counts):
if count is None:
self.stderr.write('WARNING: {} count is missing '
'for experiment {}'
.format(PATTERNS[i], experiment))
new_score = DevstarScore(
experiment=experiment,
is_bacteria_present=counts[0], area_adult=counts[1],
area_larva=counts[2], area_embryo=counts[3],
count_adult=counts[4], count_larva=counts[5],
)
# If score already exists in database, check for match
try:
previous_score = DevstarScore.objects.get(
experiment=experiment)
if not previous_score.matches_raw_fields(new_score):
raise CommandError('The DevStaR txt output does '
'not match the existing database '
'entry for Experiment {}'
.format(experiment))
except ObjectDoesNotExist:
self.stderr.write('DevStaR object not found for {}. '
'Attempting to save.'
.format(experiment))
try:
new_score.full_clean()
except ValidationError:
raise CommandError('Cleaning DevStaR object {} '
'raised ValidationError'
.format(new_score))
