def get_risk_factor_codes(self):
''' Get breast and ovarian cancer risk factor code and PRS from header lines. '''
bc_rfs = BCRiskFactors()
oc_rfs = OCRiskFactors()
bc_prs = oc_prs = None
hgt = -1
for line in self.lines:
try:
parts = line.split('=', 1)
rfnam = parts[0][2:].lower().strip() # risk factor name
rfval = parts[1].strip() # risk factor value
if rfnam == 'prs_oc': # get ovarian cancer prs
oc_prs = self.get_prs(rfval)
elif rfnam == 'prs_bc': # get breast cancer prs
bc_prs = self.get_prs(rfval)
else: # lookup breast/ovarian cancer risk factors
if rfnam == 'height':
hgt = float(rfval)
bc_rfs.add_category(rfnam, rfval)
oc_rfs.add_category(rfnam, rfval)
except Exception:
logger.error("CanRisk header format contains an error.")
raise PedigreeFileError(
"CanRisk header format contains an error in: " + line)
return (BCRiskFactors.encode(bc_rfs.cats),
OCRiskFactors.encode(oc_rfs.cats), hgt, bc_prs, oc_prs)
def test_BC_risk_factor_code(self):
'''
Test the breast cancer risk factor code generated
RFC = menarch category +
parity category * 8 +
first birth category * 40 +
OC category * 200 +
MHT category * 800 +
BMI category * 3200 +
alcohol category * 16000 +
menopause category * 128000 +
density category * 768000 +
height category * 3840000
'''
bc_risk_categories = [0 for _k in BCRiskFactors.categories.keys()]
bc_risk_categories[0] = bc.MenarcheAge.get_category('12')
rfc = 3
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
bc_risk_categories[1] = bc.Parity.get_category('1')
rfc += 2 * 8
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
bc_risk_categories[2] = bc.AgeOfFirstLiveBirth.get_category('31')
rfc += 4 * 40
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
bc_risk_categories[3] = bc.OralContraception.get_category('F:3')
rfc += 2 * 200
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
bc_risk_categories[4] = bc.MHT.get_category('C')
rfc += 3 * 800
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
bc_risk_categories[5] = bc.BMI.get_category(22.3)
rfc += 2 * 3200
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
bc_risk_categories[6] = bc.AlcoholIntake.get_category(0)
rfc += 1 * 16000
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
bc_risk_categories[7] = bc.AgeOfMenopause.get_category(52)
rfc += 4 * 128000
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
bc_risk_categories[8] = bc.MammographicDensity.get_category('1')
rfc += 1 * 768000
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
bc_risk_categories[9] = bc.Height.get_category('174.21')
rfc += 5 * 3840000
self.assertEqual(BCRiskFactors.encode(bc_risk_categories), rfc)
def test_risk_factors_inconsistent(self):
''' Test inconsistent risk factors, e.g. age of first birth specified with parity unobserved. '''
data = {
'mut_freq':
'UK',
'cancer_rates':
'UK',
'pedigree_data':
self.pedigree_data,
'user_id':
'test_XXX',
'risk_factor_code':
BCRiskFactors.encode([0, 0, 1, 0, 0, 0, 0, 0, 0, 0])
}
self.client.credentials(HTTP_AUTHORIZATION='Token ' +
BwsRiskFactors.token.key)
BwsRiskFactors.user.user_permissions.add(
Permission.objects.get(name='Can risk'))
response = self.client.post(BwsRiskFactors.url,
data,
format='multipart',
HTTP_ACCEPT="application/json")
self.assertEqual(response.status_code, status.HTTP_400_BAD_REQUEST)
content = json.loads(force_text(response.content))
self.assertTrue('Model Error' in content)
def handle(self, *args, **options):
risk_factor_code = options['factor']
categories = BCRiskFactors.decode(risk_factor_code)
for idx, cat in enumerate(categories):
name = BCRiskFactors.risk_factors[idx].__name__
print(name + " idx: " + str(cat) + " category: " +
BCRiskFactors.risk_factors[idx].cats[cat])
class OwsExtendedInputSerializer(OwsInputSerializer):
""" Other input parameters. """
risk_factor_code = serializers.IntegerField(
max_value=BCRiskFactors.get_max_factor(), min_value=0, default=0)
prs = serializers.JSONField(required=False)
def test_bounds_exceeded_u_decoding(self):
''' Test that an error is raised when a risk is above bounds - decoding '''
max_plus_1 = BCRiskFactors.encode(
list(BCRiskFactors.categories.values())) + 1
self.assertRaises(RiskFactorError, BCRiskFactors.decode, max_plus_1)
def test_round_trip(self):
''' Test encoding of risk categories and decoding returns same risk categories. '''
category1 = list(BCRiskFactors.categories.values())
category2 = BCRiskFactors.decode(BCRiskFactors.encode(category1))
self.assertListEqual(category1, category2, "round trip encode/decode")
