def field_to_schema(field):
title = force_text(field.label) if field.label else ''
description = force_text(field.help_text) if field.help_text else ''
if isinstance(field, serializers.ListSerializer):
child_schema = field_to_schema(field.child)
return coreschema.Array(items=child_schema,
title=title,
description=description)
elif isinstance(field, serializers.Serializer):
return coreschema.Object(properties=OrderedDict([
(key, field_to_schema(value))
for key, value in field.fields.items()
]),
title=title,
description=description)
elif isinstance(field, serializers.ManyRelatedField):
return coreschema.Array(items=coreschema.String(),
title=title,
description=description)
elif isinstance(field, serializers.RelatedField):
return coreschema.String(title=title, description=description)
elif isinstance(field, serializers.MultipleChoiceField):
return coreschema.Array(
items=coreschema.Enum(enum=list(field.choices.keys())),
title=title,
description=description)
elif isinstance(field, serializers.ChoiceField):
return coreschema.Enum(enum=list(field.choices.keys()),
title=title,
description=description)
elif isinstance(field, serializers.BooleanField):
return coreschema.Boolean(title=title, description=description)
elif isinstance(field, (serializers.DecimalField, serializers.FloatField)):
return coreschema.Number(title=title, description=description)
elif isinstance(field, serializers.IntegerField):
return coreschema.Integer(title=title, description=description)
if field.style.get('base_template') == 'textarea.html':
return coreschema.String(title=title,
description=description,
format='textarea')
return coreschema.String(title=title, description=description)
def get_serializer_fields(self, path, method):
"""
Return a list of `coreapi.Field` instances corresponding to any
request body input, as determined by the serializer class.
"""
view = self.view
if method not in ('PUT', 'PATCH', 'POST'):
return []
if not hasattr(view, 'get_serializer'):
return []
try:
serializer = view.get_serializer()
except exceptions.APIException:
serializer = None
warnings.warn('{}.get_serializer() raised an exception during '
'schema generation. Serializer fields will not be '
'generated for {} {}.'
.format(view.__class__.__name__, method, path))
if isinstance(serializer, serializers.ListSerializer):
return [
coreapi.Field(
name='data',
location='body',
required=True,
schema=coreschema.Array()
)
]
if not isinstance(serializer, serializers.Serializer):
return []
fields = []
for field in serializer.fields.values():
if field.read_only or isinstance(field, serializers.HiddenField):
continue
required = field.required and method != 'PATCH'
field = coreapi.Field(
name=field.field_name,
location='form',
required=required,
schema=field_to_schema(field)
)
fields.append(field)
return fields
def get_serializer_fields(self, path, method, view):
"""
Return a list of `coreapi.Field` instances corresponding to any
request body input, as determined by the serializer class.
"""
if method not in ('PUT', 'PATCH', 'POST'):
return []
if not hasattr(view, 'get_serializer'):
return []
serializer = view.get_serializer()
if isinstance(serializer, serializers.ListSerializer):
return [
coreapi.Field(
name='data',
location='body',
required=True,
schema=coreschema.Array()
)
]
if not isinstance(serializer, serializers.Serializer):
return []
fields = []
for field in serializer.fields.values():
if field.read_only or isinstance(field, serializers.HiddenField):
continue
required = field.required and method != 'PATCH'
field = coreapi.Field(
name=field.field_name,
location='form',
required=required,
schema=field_to_schema(field)
)
fields.append(field)
return fields
def field_to_schema(field):
title = force_text(field.label) if field.label else ''
description = force_text(field.help_text) if field.help_text else ''
if isinstance(field, (serializers.ListSerializer, serializers.ListField)):
child_schema = field_to_schema(field.child)
return coreschema.Array(items=child_schema,
title=title,
description=description)
elif isinstance(field, serializers.DictField):
return coreschema.Object(title=title, description=description)
elif isinstance(field, serializers.Serializer):
return coreschema.Object(properties=OrderedDict([
(key, field_to_schema(value))
for key, value in field.fields.items()
]),
title=title,
description=description)
elif isinstance(field, serializers.ManyRelatedField):
return coreschema.Array(items=coreschema.String(),
title=title,
description=description)
elif isinstance(field, serializers.PrimaryKeyRelatedField):
schema_cls = coreschema.String
model = getattr(field.queryset, 'model', None)
if model is not None:
model_field = model._meta.pk
if isinstance(model_field, models.AutoField):
schema_cls = coreschema.Integer
return schema_cls(title=title, description=description)
elif isinstance(field, serializers.RelatedField):
return coreschema.String(title=title, description=description)
elif isinstance(field, serializers.MultipleChoiceField):
return coreschema.Array(
items=coreschema.Enum(enum=list(field.choices)),
title=title,
description=description)
elif isinstance(field, serializers.ChoiceField):
return coreschema.Enum(enum=list(field.choices),
title=title,
description=description)
elif isinstance(field, serializers.BooleanField):
return coreschema.Boolean(title=title, description=description)
elif isinstance(field, (serializers.DecimalField, serializers.FloatField)):
return coreschema.Number(title=title, description=description)
elif isinstance(field, serializers.IntegerField):
return coreschema.Integer(title=title, description=description)
elif isinstance(field, serializers.DateField):
return coreschema.String(title=title,
description=description,
format='date')
elif isinstance(field, serializers.DateTimeField):
return coreschema.String(title=title,
description=description,
format='date-time')
elif isinstance(field, serializers.JSONField):
return coreschema.Object(title=title, description=description)
if field.style.get('base_template') == 'textarea.html':
return coreschema.String(title=title,
description=description,
format='textarea')
return coreschema.String(title=title, description=description)
def test_authenticated_request(self):
client = APIClient()
client.force_authenticate(MockUser())
response = client.get('/', HTTP_ACCEPT='application/coreapi+json')
assert response.status_code == 200
expected = coreapi.Document(
url='http://testserver/',
title='Example API',
content={
'example': {
'list':
coreapi.Link(
url='/example/',
action='get',
fields=[
coreapi.Field(
'page',
required=False,
location='query',
schema=coreschema.Integer(
title='Page',
description=
'A page number within the paginated result set.'
)),
coreapi.Field(
'page_size',
required=False,
location='query',
schema=coreschema.Integer(
title='Page size',
description=
'Number of results to return per page.')),
coreapi.Field(
'ordering',
required=False,
location='query',
schema=coreschema.String(
title='Ordering',
description=
'Which field to use when ordering the results.'
))
]),
'create':
coreapi.Link(
url='/example/',
action='post',
encoding='application/json',
fields=[
coreapi.Field(
'a',
required=True,
location='form',
schema=coreschema.String(
title='A',
description='A field description')),
coreapi.Field('b',
required=False,
location='form',
schema=coreschema.String(title='B'))
]),
'read':
coreapi.Link(
url='/example/{id}/',
action='get',
fields=[
coreapi.Field('id',
required=True,
location='path',
schema=coreschema.String()),
coreapi.Field(
'ordering',
required=False,
location='query',
schema=coreschema.String(
title='Ordering',
description=
'Which field to use when ordering the results.'
))
]),
'custom_action':
coreapi.Link(
url='/example/{id}/custom_action/',
action='post',
encoding='application/json',
description='A description of custom action.',
fields=[
coreapi.Field('id',
required=True,
location='path',
schema=coreschema.String()),
coreapi.Field('c',
required=True,
location='form',
schema=coreschema.String(title='C')),
coreapi.Field('d',
required=False,
location='form',
schema=coreschema.String(title='D')),
]),
'custom_action_with_list_fields':
coreapi.Link(
url='/example/{id}/custom_action_with_list_fields/',
action='post',
encoding='application/json',
description=
'A custom action using both list field and list serializer in the serializer.',
fields=[
coreapi.Field('id',
required=True,
location='path',
schema=coreschema.String()),
coreapi.Field('a',
required=True,
location='form',
schema=coreschema.Array(
title='A',
items=coreschema.Integer())),
coreapi.Field('b',
required=True,
location='form',
schema=coreschema.Array(
title='B',
items=coreschema.String())),
]),
'custom_list_action':
coreapi.Link(url='/example/custom_list_action/',
action='get'),
'custom_list_action_multiple_methods': {
'read':
coreapi.Link(
url='/example/custom_list_action_multiple_methods/',
action='get'),
'create':
coreapi.Link(
url='/example/custom_list_action_multiple_methods/',
action='post')
},
'update':
coreapi.Link(
url='/example/{id}/',
action='put',
encoding='application/json',
fields=[
coreapi.Field('id',
required=True,
location='path',
schema=coreschema.String()),
coreapi.Field(
'a',
required=True,
location='form',
schema=coreschema.String(
title='A',
description=('A field description'))),
coreapi.Field('b',
required=False,
location='form',
schema=coreschema.String(title='B')),
coreapi.Field(
'ordering',
required=False,
location='query',
schema=coreschema.String(
title='Ordering',
description=
'Which field to use when ordering the results.'
))
]),
'partial_update':
coreapi.Link(
url='/example/{id}/',
action='patch',
encoding='application/json',
fields=[
coreapi.Field('id',
required=True,
location='path',
schema=coreschema.String()),
coreapi.Field(
'a',
required=False,
location='form',
schema=coreschema.String(
title='A',
description='A field description')),
coreapi.Field('b',
required=False,
location='form',
schema=coreschema.String(title='B')),
coreapi.Field(
'ordering',
required=False,
location='query',
schema=coreschema.String(
title='Ordering',
description=
'Which field to use when ordering the results.'
))
]),
'delete':
coreapi.Link(
url='/example/{id}/',
action='delete',
fields=[
coreapi.Field('id',
required=True,
location='path',
schema=coreschema.String()),
coreapi.Field(
'ordering',
required=False,
location='query',
schema=coreschema.String(
title='Ordering',
description=
'Which field to use when ordering the results.'
))
])
}
})
assert response.data == expected
class SubmitView(APIView):
"""
提交
"""
permission_classes = (IsAuthenticated,)
schema = AutoSchema(manual_fields=[
coreapi.Field(name='problem',
required=True,
location='form',
schema=coreschema.Integer(title='problem',
description='要提交的题目ID')),
coreapi.Field(name='submit_files',
required=True,
location='form',
schema=coreschema.Array(title='submit_files',
items=coreschema.Integer,
description='要提交的文件（代码等）')),
])
def post(self, request, *args):
# Fix bug: must check permission first
self.check_permissions(request)
# put the user segment in, ref: BaseSerializer docstring
# Fix bug: AttributeError: This QueryDict instance is immutable
# ref: https://stackoverflow.com/questions/44717442/this-querydict-instance-is-immutable
data = request.data.copy()
data['user'] = request.user.id
serializer = SubmissionSerializer(data=data)
# print(request.data)
# print(serializer.initial_data)
try:
serializer.is_valid(True)
# (Optional) Checking for deadline time
ddl = Problem.objects.filter(id=data['problem'])[0].deadline_time
if ddl is not None and ddl < django.utils.timezone.now():
# Whoops, you dare submitting it over ddl!
return Response("You've submitted it after deadline! {}".format(str(ddl)),
status.HTTP_400_BAD_REQUEST)
subm = serializer.save()
# Instantiate judge task for all testcases
# Get all test cases related to this problem
prob_id = serializer.data['problem']
subm_id = subm.id
# print("{} {}".format(prob_id, subm_id))
prob = Problem.objects.filter(id=prob_id).first()
if prob == None:
return Response('No such problem', status.HTTP_404_NOT_FOUND)
for case in prob.get_testcases():
# Create a new SubmissionResult structure
subm_res = SubmissionResult.objects.create(
status='PENDING',
submission=subm,
testcase=case,
grade=0,
log="",
app_data="",
possible_failure='NA'
)
do_judge_task.delay(subm_id, case.id, subm_res.id)
#do_judge_task(serializer.data['id'], serializer.data[''])
return Response(serializer._data, status.HTTP_201_CREATED)
except Exception as e:
return Response(str(e), status.HTTP_500_INTERNAL_SERVER_ERROR)
class BCTenYrView(APIView, ModelWebServiceMixin):
"""
Ten year breast cancer risks calculation Web-Service
"""
renderer_classes = (
JSONRenderer,
TemplateHTMLRenderer,
)
serializer_class = BCTenYrSerializer
authentication_classes = (
SessionAuthentication,
BasicAuthentication,
TokenAuthentication,
)
permission_classes = (IsAuthenticated, )
throttle_classes = (BurstRateThrottle, SustainedRateThrottle,
EndUserIDRateThrottle)
model = settings.BC_MODEL
if coreapi is not None and coreschema is not None:
fields = ModelWebServiceMixin.get_fields(model)
fields.insert(
0,
coreapi.Field(
name="tenyr_ages",
required=True,
location='form',
schema=coreschema.Array(
title="tenyr_ages",
description='List of ages to calculate the 10-year risks',
min_items=1,
unique_items=True)))
schema = ManualSchema(fields=fields,
encoding="application/json",
description="""
Ten year breast cancer risks calculations as per those given for the ages 40-49
(https://canrisk.atlassian.net/wiki/x/NwDCAg). The web-service takes a list of
ages to calculate the 10-year risks for, e.g. [25, 26, 27, 28, 29] or [29].
""")
# @profile("profile_bws.profile")
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(',')]
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,
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 = 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)
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("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("BCTenYr :: "+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 test_schema_for_regular_views(self):
"""
Ensure that AutoField many to many fields are output as Integer.
"""
generator = SchemaGenerator(title='Example API', patterns=self.patterns)
schema = generator.get_schema()
expected = coreapi.Document(
url='',
title='Example API',
content={
'example': {
'create': coreapi.Link(
url='/example/',
action='post',
encoding='application/json',
fields=[
coreapi.Field('name', required=True, location='form', schema=coreschema.String(title='Name')),
coreapi.Field('targets', required=True, location='form', schema=coreschema.Array(title='Targets', items=coreschema.Integer())),
]
)
}
}
)
assert schema == expected
