def test_niceness(self):
""" Test niceness level for pedigree with sibling and large pedigree. """
pedigree = deepcopy(self.pedigree)
self.assertEqual(Predictions._get_niceness(pedigree, factor=1), len(pedigree.people))
self.assertEqual(Predictions._get_niceness(pedigree, factor=0.01), 19)
# sister
target = pedigree.get_target()
sister = Female("FAM1", "F01", "0011", target.fathid, target.mothid, age="22",
yob=str(self.year-23), cancers=Cancers(bc1=Cancer("20")))
pedigree.people.append(sister)
self.assertEqual(Predictions._get_niceness(pedigree), 1)
def post(self, request):
serializer = self.serializer_class(data=request.data)
if serializer.is_valid(raise_exception=True):
validated_data = serializer.validated_data
pf = PedigreeFile(validated_data.get('pedigree_data'))
model_settings = settings.BC_MODEL
params = ModelParams.factory(validated_data, model_settings)
tenyr_ages = re.sub("[\[\]]", "", validated_data.get('tenyr_ages'))
tenyr_ages = [int(item.strip()) for item in tenyr_ages.split(',')]
logger.debug(tenyr_ages)
output = {
"timestamp": datetime.datetime.now(),
"mutation_frequency": {
params.population: params.mutation_frequency
},
"mutation_sensitivity": params.mutation_sensitivity,
"cancer_incidence_rates": params.cancer_rates,
"pedigree_result": []
}
risk_factor_code = validated_data.get('risk_factor_code', 0)
prs = validated_data.get('prs', None)
if prs is not None:
prs = Prs(prs.get('alpha'), prs.get('zscore'))
try:
warnings = PedigreeFile.validate(pf.pedigrees)
if len(warnings) > 0:
output['warnings'] = warnings
except ValidationError as e:
logger.error(e)
return JsonResponse(e.detail,
content_type="application/json",
status=status.HTTP_400_BAD_REQUEST)
# note limit username string length used here to avoid paths too long for model code
cwd = tempfile.mkdtemp(prefix=str(request.user)[:20] + "_",
dir=settings.CWD_DIR)
try:
for pedi in pf.pedigrees:
this_params = deepcopy(params)
# check if Ashkenazi Jewish status set & correct mutation frequencies
if pedi.is_ashkn() and not REGEX_ASHKN.match(
params.population):
msg = 'mutation frequencies set to Ashkenazi Jewish population values ' \
'for family ('+pedi.famid+') as a family member has Ashkenazi Jewish status.'
logger.debug(
'mutation frequencies set to Ashkenazi Jewish population values'
)
if 'warnings' in output:
output['warnings'].append(msg)
else:
output['warnings'] = [msg]
this_params.population = 'Ashkenazi'
this_params.mutation_frequency = model_settings[
'MUTATION_FREQUENCIES']['Ashkenazi']
if isinstance(pedi, CanRiskPedigree):
# for canrisk format files check if risk factors and/or prs set in the header
mname = model_settings['NAME']
if 'risk_factor_code' not in request.data.keys():
risk_factor_code = pedi.get_rfcode(mname)
if prs is None or len(pf.pedigrees) > 1:
prs = pedi.get_prs(mname)
calcs = Predictions(pedi,
model_params=this_params,
risk_factor_code=risk_factor_code,
prs=prs,
run_risks=False,
cwd=cwd,
request=request,
model_settings=model_settings)
calcs.niceness = Predictions._get_niceness(calcs.pedi)
calcs.ten_yr_cancer_risk = []
for tenyr in tenyr_ages:
ten_yr_risk, _v = RangeRisk(calcs, int(tenyr),
int(tenyr + 10),
"10 YR RANGE").get_risk()
if ten_yr_risk is not None:
calcs.ten_yr_cancer_risk.append(ten_yr_risk[0])
# Add input parameters and calculated results as attributes to 'this_pedigree'
this_pedigree = {}
this_pedigree["family_id"] = pedi.famid
this_pedigree["proband_id"] = pedi.get_target().pid
this_pedigree["risk_factors"] = self.get_risk_factors(
model_settings, risk_factor_code)
if prs is not None:
this_pedigree["prs"] = {
'alpha': prs.alpha,
'zscore': prs.zscore
}
this_pedigree["mutation_frequency"] = {
this_params.population: this_params.mutation_frequency
}
self.add_attr("version", output, calcs, output)
self.add_attr("ten_yr_cancer_risk", this_pedigree, calcs,
output)
output["pedigree_result"].append(this_pedigree)
except ValidationError as e:
logger.error(e)
return JsonResponse(e.detail,
content_type="application/json",
status=status.HTTP_400_BAD_REQUEST,
safe=False)
finally:
shutil.rmtree(cwd)
output_serialiser = OutputSerializer(output)
return Response(output_serialiser.data,
template_name='result_tab_gp.html')
return Response(serializer.errors, status=status.HTTP_400_BAD_REQUEST)