def test_affected_unknown(self):
""" Test including affected unknown for mother of target to show it increases breast cancer risk. """
pedigree = deepcopy(self.pedigree)
target = pedigree.get_target()
mother = pedigree.get_person(target.mothid)
mother.yob = str(self.year - 55)
mother.age = "55"
calcs1 = Predictions(pedigree, cwd=self.cwd)
def get_c80(calcs):
for c in calcs.cancer_risks:
if c.get('age') == 80:
return c['breast cancer risk']['decimal']
return None
# add affected unknown to mother
mother.cancers = Cancers(bc1=Cancer("AU"),
bc2=Cancer(),
oc=Cancer(),
prc=Cancer(),
pac=Cancer())
calcs2 = Predictions(pedigree, cwd=self.cwd)
self.assertGreater(
get_c80(calcs2), get_c80(calcs1),
'Mother affected unknown increases BC risk in target')
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 test_calcs_validation_err(self):
""" Test invalid calculation type raise ValidationError. """
target = Female("FAM1", "F0", "001", "002", "003", target="1", age="20",
yob=str(date.today().year-20), gtests=CanRiskGeneticTests.default_factory())
pedigree = CanRiskPedigree(people=[target])
with self.assertRaisesRegex(ValidationError, r"Unknown calculation requested: dribble"):
Predictions(pedigree, model_settings=settings.OC_MODEL, calcs=['dribble'])
def test_bws_model_err(self):
''' Test ModelError raised because of pedigree file with only one twin. '''
target = Female("FAM1", "F0", "001", "002", "003", target="1", age="20", mztwin="1",
yob=str(date.today().year-20), gtests=CanRiskGeneticTests.default_factory())
pedigree = CanRiskPedigree(people=[target])
with self.assertRaisesRegex(ModelError, r"ERRORS IN THE PEDIGREE FILE"):
Predictions(pedigree)
def test_subproces_err(self):
""" Test subprocess raises an error when the fortran can not be run. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
with self.assertRaises(FileNotFoundError):
model_settings = settings.BC_MODEL
model_settings['HOME'] = 'xyz'
Predictions(pedigree, cwd=self.cwd, model_settings=model_settings)
def test_10yr_range_risk(self):
""" Test ten year range (40-49) risk calculation matches the risk to 50 for a 40 year old. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
calcs1 = Predictions(pedigree, cwd=self.cwd)
t = pedigree.get_target()
t.age = '40'
calcs2 = Predictions(pedigree, cwd=self.cwd)
c50 = None
for c in calcs2.cancer_risks:
if c.get('age') == 50:
c50 = c
self.assertEqual(
calcs1.ten_yr_cancer_risk[0]['breast cancer risk']['decimal'],
c50['breast cancer risk']['decimal'])
def test_pedigree_range_baseline(self):
""" Test pedigree for baseline time range (e.g. lifetime, 10yr range) risk calculation. """
p1 = deepcopy(self.pedigree)
PedigreeFile.validate(p1)
calcs = Predictions(p1, cwd=self.cwd, run_risks=False)
range_baseline = RangeRiskBaseline(calcs, 40, 50, "10 YR RANGE BASELINE")
p2 = range_baseline._get_pedi()
self.assertEqual(len(p2.people), 1)
self.assertEqual(p2.get_target().age, 40)
self.assertNotEqual(p1.get_target().age, p2.get_target().age)
def test_pedigree_remaining_lifetime(self):
""" Test pedigree for remaining lifetime risk calculation. """
p1 = deepcopy(self.pedigree)
PedigreeFile.validate(p1)
calcs = Predictions(p1, cwd=self.cwd, run_risks=False)
self.assertTrue(calcs.pedi.is_carrier_probs_viable())
self.assertTrue(calcs.pedi.is_risks_calc_viable())
remaining_life = RemainingLifetimeRisk(calcs)
p2 = remaining_life._get_pedi()
self.assertEqual(len(p1.people), len(p2.people))
self.assertEqual(p1.get_target().age, p2.get_target().age)
def test_calculations2(self):
""" Test prediction of cancer risk and mutation probability. """
pedigree = deepcopy(self.pedigree)
target = pedigree.get_target()
target.age = str(int(target.age) + 43)
# sister
# diagnoses = CancerDiagnoses(bc1=Cancer("20"), bc2=Cancer(), oc=Cancer(),
# prc=Cancer(), pac=Cancer())
# sister = Female("FAM1", "F01", "0011", target.fathid, target.mothid, age="22", yob=str(self.year-23),
# cancers=Cancers(diagnoses=diagnoses))
# pedigree.people.append(sister)
# parents
mother = pedigree.get_person(target.mothid)
mother.yob = str(self.year - 84)
mother.age = "85"
mother.cancers = Cancers(bc1=Cancer("52"),
bc2=Cancer(),
oc=Cancer(),
prc=Cancer(),
pac=Cancer())
# maternal grandparents
(_maternal_grandfather,
maternal_grandmother) = pedigree.add_parents(mother)
maternal_grandmother.age = "81"
maternal_grandmother.yob = "1912"
maternal_grandmother.dead = "1"
maternal_grandmother.cancers = Cancers(bc1=Cancer("42"),
bc2=Cancer(),
oc=Cancer(),
prc=Cancer(),
pac=Cancer())
PedigreeFile.validate(pedigree)
calcs = Predictions(pedigree, cwd=self.cwd)
# each gene should have a mutation probability plus a result for no mutations
for mp in calcs.mutation_probabilties:
key = list(mp.keys())[0]
self.assertTrue(key in settings.BC_MODEL['GENES']
or key == "no mutation")
self.assertEqual(len(calcs.mutation_probabilties),
len(settings.BC_MODEL['GENES']) + 1)
# risks calculated at different ages:
self.assertEqual(len(calcs.cancer_risks), 9)
self.assertTrue([c.get('age') for c in calcs.cancer_risks] ==
[64, 65, 66, 67, 68, 70, 73, 75, 80])
def test_lifetime_risk(self):
""" Test lifetime risk calculation matches the risk to 80 for a 20 year old. """
pedigree = deepcopy(self.pedigree)
t = pedigree.get_target()
t.age = '20'
PedigreeFile.validate(pedigree)
calcs = Predictions(pedigree, cwd=self.cwd)
c80 = None
for c in calcs.cancer_risks:
if c.get('age') == 80:
c80 = c
self.assertEqual(calcs.lifetime_cancer_risk[0]['breast cancer risk']['decimal'],
c80['breast cancer risk']['decimal'])
self.assertEqual(calcs.lifetime_cancer_risk[0]['ovarian cancer risk']['decimal'],
c80['ovarian cancer risk']['decimal'])
def test_calculations(self):
""" Test prediction of cancer risk and mutation probability. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
calcs = Predictions(pedigree, cwd=self.cwd)
# each gene should have a mutation probability plus a result for no mutations
for mp in calcs.mutation_probabilties:
key = list(mp.keys())[0]
self.assertTrue(key in settings.BC_MODEL['GENES'] or key == "no mutation")
self.assertEqual(len(calcs.mutation_probabilties), len(settings.BC_MODEL['GENES']) + 1)
# risks calculated at 16 different ages:
self.assertEqual(len(calcs.cancer_risks), 16)
self.assertTrue([c.get('age') for c in calcs.cancer_risks] ==
[21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80])
def test_incidence_rates(self):
""" Test prediction of cancer risk and mutation probability for different incidence rates. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
target = pedigree.get_target()
target.age = 78
crates = settings.BC_MODEL['CANCER_RATES']
for cancer_rates in crates.values():
calcs = Predictions(pedigree, cwd=self.cwd, cancer_rates=cancer_rates)
# each gene should have a mutation probability plus a result for no mutations
self.assertEqual(len(calcs.mutation_probabilties), len(settings.BC_MODEL['GENES']) + 1)
# risks calculated at different ages:
self.assertTrue([c.get('age') for c in calcs.cancer_risks] ==
[79, 80])
def run_calc(cls, can, pedigree, calcs=None, cwd=None):
""" Run rrisk calculations """
msettings = settings.BC_MODEL if can == 'breast' else settings.OC_MODEL
mparams = ModelParams(
mutation_frequency=msettings['MUTATION_FREQUENCIES']["UK"],
mutation_sensitivity=msettings['GENETIC_TEST_SENSITIVITY'])
calcs = Predictions(pedigree,
cwd=cwd,
model_settings=msettings,
model_params=mparams,
calcs=calcs)
c80 = None
for c in calcs.cancer_risks:
if c.get('age') == 80:
c80 = c
return c80[can +
' cancer risk']['decimal'], calcs.lifetime_cancer_risk[0][
can + ' cancer risk']['decimal']
def test_mutation_frequencies(self):
""" Test prediction of cancer risk and mutation probability for different mutation frequencies. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
target = pedigree.get_target()
target.age = 78
mutation_frequencies = settings.BC_MODEL['MUTATION_FREQUENCIES']
for mf in mutation_frequencies.keys():
if mf == 'Custom':
continue
params = ModelParams(mutation_frequency=mutation_frequencies[mf])
calcs = Predictions(pedigree, cwd=self.cwd, model_params=params)
# each gene should have a mutation probability plus a result for no mutations
self.assertEqual(len(calcs.mutation_probabilties), len(settings.BC_MODEL['GENES']) + 1)
# risks calculated at different ages:
self.assertTrue([c.get('age') for c in calcs.cancer_risks] ==
[79, 80])
def test_ovarian_calculations(self):
""" Test prediction of cancer risk and mutation probability. """
target = Female("FAM1",
"F0",
"001",
"002",
"003",
target="1",
age="20",
yob=str(self.year - 20),
cancers=Cancers(),
gtests=CanRiskGeneticTests.default_factory())
pedigree = CanRiskPedigree(people=[target])
# parents
(_father, _mother) = pedigree.add_parents(
target, gtests=CanRiskGeneticTests.default_factory())
PedigreeFile.validate(pedigree)
params = ModelParams(
mutation_frequency=settings.OC_MODEL['MUTATION_FREQUENCIES']["UK"],
mutation_sensitivity=settings.OC_MODEL['GENETIC_TEST_SENSITIVITY'])
calcs = Predictions(pedigree,
cwd=self.cwd,
model_params=params,
model_settings=settings.OC_MODEL,
calcs=[])
# each gene should have a mutation probability plus a result for no mutations
for mp in calcs.mutation_probabilties:
key = list(mp.keys())[0]
self.assertTrue(key in settings.OC_MODEL['GENES']
or key == "no mutation")
self.assertEqual(len(calcs.mutation_probabilties),
len(settings.OC_MODEL['GENES']) + 1)
# risks calculated at 16 different ages:
self.assertEqual(len(calcs.cancer_risks), 16)
self.assertTrue(
[c.get('age') for c in calcs.cancer_risks] ==
[21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80])
def post_to_model(self, request, model_settings):
serializer = self.serializer_class(data=request.data)
if serializer.is_valid(raise_exception=True):
validated_data = serializer.validated_data
pedigree_data = validated_data.get('pedigree_data')
pf = PedigreeFile(pedigree_data)
population = validated_data.get('mut_freq', 'UK')
cancer_rates = model_settings['CANCER_RATES'].get(
validated_data.get('cancer_rates'))
if population != 'Custom':
mutation_frequency = model_settings['MUTATION_FREQUENCIES'][
population]
else:
mutation_frequency = {}
for gene in model_settings['GENES']:
try:
mutation_frequency[gene] = float(
validated_data.get(gene.lower() +
'_mut_frequency'))
except TypeError:
raise NotAcceptable("Invalid mutation frequency for " +
gene + ".")
gts = model_settings['GENETIC_TEST_SENSITIVITY']
mutation_sensitivity = {
k: float(
validated_data.get(k.lower() + "_mut_sensitivity", gts[k]))
for k in gts.keys()
}
output = {
"timestamp": datetime.datetime.now(),
"mutation_frequency": {
population: mutation_frequency
},
"mutation_sensitivity": mutation_sensitivity,
"cancer_incidence_rates": cancer_rates,
"pedigree_result": []
}
if request.user.has_perm('boadicea_auth.can_risk'):
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'))
else:
if validated_data.get('risk_factor_code', 0) > 0:
logger.warning(
'risk factor code parameter provided without the correct permissions'
)
if validated_data.get('prs', 0) != 0:
logger.warning(
'polygenic risk score parameter provided without the correct permissions'
)
risk_factor_code = 0
prs = None
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 to long for model code
cwd = tempfile.mkdtemp(prefix=str(request.user)[:20] + "_",
dir=settings.CWD_DIR)
try:
for pedi in pf.pedigrees:
this_pedigree = {}
this_pedigree["family_id"] = pedi.famid
this_pedigree["proband_id"] = pedi.get_target().pid
this_mutation_frequency = mutation_frequency
this_population = population
# check if Ashkenazi Jewish status set & correct mutation frequencies
if pedi.is_ashkn():
if not REGEX_ASHKN.match(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_population = 'Ashkenazi'
this_mutation_frequency = model_settings[
'MUTATION_FREQUENCIES'][this_population]
mname = model_settings['NAME']
if request.user.has_perm(
'boadicea_auth.can_risk') and isinstance(
pedi, CanRiskPedigree):
# for canrisk format files check if risk factors and/or prs set in the header
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)
if request.user.has_perm('boadicea_auth.can_risk'):
# add risk factors and prs used for this pedigree
this_pedigree["risk_factors"] = self.get_risk_factors(
model_settings, risk_factor_code)
logger.debug(mname + ' risk factor code ' +
str(risk_factor_code))
if prs is not None:
this_pedigree["prs"] = {
'alpha': prs.alpha,
'zscore': prs.zscore
}
logger.debug(mname + ' PRS alpha:' +
str(this_pedigree["prs"]))
calcs = Predictions(
pedi,
mutation_frequency=this_mutation_frequency,
mutation_sensitivity=mutation_sensitivity,
cancer_rates=cancer_rates,
risk_factor_code=risk_factor_code,
prs=prs,
cwd=cwd,
request=request,
model_settings=model_settings)
# Add input parameters and calculated results as attributes to 'this_pedigree'
this_pedigree["mutation_frequency"] = {
this_population: this_mutation_frequency
}
self.add_attr("version", output, calcs, output)
self.add_attr("mutation_probabilties", this_pedigree,
calcs, output)
self.add_attr("cancer_risks", this_pedigree, calcs, output)
self.add_attr("baseline_cancer_risks", this_pedigree,
calcs, output)
self.add_attr("lifetime_cancer_risk", this_pedigree, calcs,
output)
self.add_attr("baseline_lifetime_cancer_risk",
this_pedigree, calcs, output)
self.add_attr("ten_yr_cancer_risk", this_pedigree, calcs,
output)
self.add_attr("baseline_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:
if (not request.user.has_perm('boadicea_auth.evaluation') and
not request.user.has_perm('boadicea_auth.evaluation1b')
):
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)
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)
def post_to_model(self, request, model_settings):
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'))
params = ModelParams.factory(validated_data, model_settings)
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": []
}
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:
risk_factor_code = 0
this_params = deepcopy(params)
# check if Ashkenazi Jewish status set & correct mutation frequencies
if pedi.is_ashkn() and not settings.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.isashk = True
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']
risk_factor_code = pedi.get_rfcode(mname)
if prs is None or len(pf.pedigrees) > 1:
prs = pedi.get_prs(mname)
this_hgt = (pedi.hgt if hasattr(pedi, 'hgt') else -1)
calcs = Predictions(pedi,
model_params=this_params,
risk_factor_code=risk_factor_code,
hgt=this_hgt,
prs=prs,
cwd=cwd,
request=request,
model_settings=model_settings)
# 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)
this_pedigree["risk_factors"][_(
'Height (cm)')] = this_hgt if this_hgt != -1 else "-"
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("mutation_probabilties", this_pedigree,
calcs, output)
self.add_attr("cancer_risks", this_pedigree, calcs, output)
self.add_attr("baseline_cancer_risks", this_pedigree,
calcs, output)
self.add_attr("lifetime_cancer_risk", this_pedigree, calcs,
output)
self.add_attr("baseline_lifetime_cancer_risk",
this_pedigree, calcs, output)
self.add_attr("ten_yr_cancer_risk", this_pedigree, calcs,
output)
self.add_attr("baseline_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)
# print(model_settings['NAME']+" :: "+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)