def ws_prs(self, url, cancer='breast'):
''' Test affect of including the PRS. '''
data = {
'mut_freq': 'UK',
'cancer_rates': 'UK',
'pedigree_data': self.pedigree_data,
'user_id': 'test_XXX'
}
self.client.credentials(HTTP_AUTHORIZATION='Token ' +
WSRiskFactors.token.key)
response = self.client.post(url,
data,
format='multipart',
HTTP_ACCEPT="application/json")
self.assertEqual(response.status_code, status.HTTP_200_OK)
cancer_risks1 = json.loads(force_text(
response.content))['pedigree_result'][0]['cancer_risks']
# add PRS
data['prs'] = json.dumps({'alpha': 0.45, 'zscore': 2.652})
response = self.client.post(url,
data,
format='multipart',
HTTP_ACCEPT="application/json")
self.assertEqual(response.status_code, status.HTTP_200_OK)
cancer_risks2 = json.loads(force_text(
response.content))['pedigree_result'][0]['cancer_risks']
self.assertLess(cancer_risks1[0][f'{cancer} cancer risk']['decimal'],
cancer_risks2[0][f'{cancer} cancer risk']['decimal'])
def ws_risk_factor(self, url, bmi, cancer='breast'):
''' Test affect of including the risk factors. '''
data = {
'mut_freq': 'UK',
'cancer_rates': 'UK',
'pedigree_data': self.pedigree_data,
'user_id': 'test_XXX'
}
self.client.credentials(HTTP_AUTHORIZATION='Token ' +
WSRiskFactors.token.key)
response = self.client.post(url,
data,
format='multipart',
HTTP_ACCEPT="application/json")
self.assertEqual(response.status_code, status.HTTP_200_OK)
cancer_risks1 = json.loads(force_text(
response.content))['pedigree_result'][0]['cancer_risks']
# add BMI
data['pedigree_data'] = self.pedigree_data.replace(
"##CanRisk 2.0", f"##CanRisk 2.0\n##BMI={bmi}")
response = self.client.post(url,
data,
format='multipart',
HTTP_ACCEPT="application/json")
self.assertEqual(response.status_code, status.HTTP_200_OK)
cancer_risks2 = json.loads(force_text(
response.content))['pedigree_result'][0]['cancer_risks']
self.assertLess(cancer_risks1[0][f'{cancer} cancer risk']['decimal'],
cancer_risks2[0][f'{cancer} cancer risk']['decimal'])
def fallback_schema_from_field(self, field):
""" Fallback schema for field that isn't inspected properly by DRF
and probably won't land in upstream canon due to its hacky nature only for doc purposes
"""
title = force_text(field.label) if field.label else ''
description = force_text(field.help_text) if field.help_text else ''
# since we can't really inspect dictfield and jsonfield, at least display object as type
# instead of string
if isinstance(field, (serializers.DictField, serializers.JSONField)):
return coreschema.Object(properties={},
title=title,
description=description)
def get_path_fields(self, path, method, view):
"""
Return a list of `coreapi.Field` instances corresponding to any
templated path variables.
"""
model = getattr(getattr(view, 'queryset', None), 'model', None)
fields = []
for variable in uritemplate.variables(path):
if variable == 'version':
continue
title = ''
description = ''
schema_cls = coreschema.String
kwargs = {}
if model is not None:
# Attempt to infer a field description if possible.
try:
model_field = model._meta.get_field(variable)
except:
model_field = None
if model_field is not None and model_field.verbose_name:
title = force_text(model_field.verbose_name)
if model_field is not None and model_field.help_text:
description = force_text(model_field.help_text)
elif model_field is not None and model_field.primary_key:
description = get_pk_description(model, model_field)
if hasattr(view, 'lookup_value_regex'
) and view.lookup_field == variable:
kwargs['pattern'] = view.lookup_value_regex
elif isinstance(model_field, models.AutoField):
schema_cls = coreschema.Integer
field = Field(name=variable,
location='path',
required=True,
schema=schema_cls(title=title,
description=description,
**kwargs))
fields.append(field)
return fields
def activate(request, uidb64, token):
account_activation_token = AccountActivationTokenGenerator()
try:
uid = force_text(urlsafe_base64_decode(uidb64))
user = User.objects.get(pk=uid)
except (TypeError, ValueError, OverflowError, User.DoesNotExist):
user = None
if user is not None and account_activation_token.check_token(user, token):
user.is_active = True
user.save()
return Response(
{"message": "You have activated account, now you can Log In!"})
def get_path_parameters(self, path, view_cls):
"""Return a list of Parameter instances corresponding to any templated path variables.
:param str path: templated request path
:param type view_cls: the view class associated with the path
:return: path parameters
:rtype: list[openapi.Parameter]
"""
parameters = []
model = getattr(getattr(view_cls, 'queryset', None), 'model', None)
for variable in uritemplate.variables(path):
pattern = None
type = openapi.TYPE_STRING
description = None
if model is not None:
# Attempt to infer a field description if possible.
try:
model_field = model._meta.get_field(variable)
except Exception: # pragma: no cover
model_field = None
if model_field is not None and model_field.help_text:
description = force_text(model_field.help_text)
elif model_field is not None and model_field.primary_key:
description = get_pk_description(model, model_field)
if hasattr(view_cls, 'lookup_value_regex') and getattr(
view_cls, 'lookup_field', None) == variable:
pattern = view_cls.lookup_value_regex
elif isinstance(model_field, django.db.models.AutoField):
type = openapi.TYPE_INTEGER
field = openapi.Parameter(
name=variable,
required=True,
in_=openapi.IN_PATH,
type=type,
pattern=pattern,
description=description,
)
parameters.append(field)
return parameters
def mockreturn(self, request):
codec = CoreJSONCodec()
body = force_text(request.body)
content = codec.encode(Document(content={'data': json.loads(body)}))
return MockResponse(content)
