def rate_in(self, rate_type):
filtered_rates = self.rates.filter(rate_type=rate_type)
if filtered_rates.count() > 0:
return filtered_rates[0]
else:
rf = AgeSpecificRateFunction(disease=self.disease, region=self.region,
sex=self.sex, rate_type=rate_type,
notes='From Disease Model %d' % self.id)
rf.save()
self.rates.add(rf)
return rf
def handle(self, *fnames, **options):
import csv
if len(fnames) != 1:
raise CommandError('a single .csv file is required as input.')
fname = fnames[0]
print "adding rates from %s" % fname
disease, created = Disease.objects.get_or_create(name='all causes')
rate_counter = 0
csv_file = csv.reader(open(fname))
headings = csv_file.next()
# check if the headings are as expected, complain if not
if headings != ['', 'year', 'agegroup', 'sex', 'gbdregion', 'mortalityrate']:
raise CommandError('csv file headings not as expected.')
rates_for_region = {}
for ii,row in enumerate(csv_file):
params = {}
params['rate_type'] = 'all-cause mortality data'
params['disease'], created = Disease.objects.get_or_create(name='all-cause mortality')
# only load mortality data from 1990 and 2005
if not (row[1] in ['1990', '2005']):
continue
params['epoch_start'] = int(row[1])
params['epoch_end'] = int(row[1])
if row[2] == '0_1':
params['age_start'] = 0
params['age_end'] = 0
elif row[2] == '85above':
params['age_start'] = 85
params['age_end'] = -99
else:
ages = row[2].split('-')
params['age_start'] = int(ages[0])
params['age_end'] = int(ages[1])
params['sex'] = row[3]
region_name = smart_unicode(row[4].strip(), errors='ignore')
params['country'] = 'all in %s' % region_name
params['region'], created = Region.objects.get_or_create(name=region_name)
if row[5] == 'NA':
continue
params['numerator'] = float(row[5])*10.e7
params['denominator'] = 10.e7
rate_data, created = Rate.objects.get_or_create(**params)
rate_counter += created
key = str(params['region']) + params['sex'] + str(params['epoch_start'])
if not rates_for_region.has_key(key):
rates_for_region[key] = []
rates_for_region[key] += [rate_data]
print "added %d rates" % rate_counter
for rates in rates_for_region.values():
if len(rates) > 0:
r = rates[0]
rf = AgeSpecificRateFunction(disease=r.disease, region=r.region, rate_type=r.rate_type, sex=r.sex)
rf.save()
rf.rates = rates
rf.save()
print 'created age-specific rate function %d' % rf.id
