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 test_field_to_schema(self):
label = 'Test label'
help_text = 'This is a helpful test text'
cases = [
# tuples are ([field], [expected schema])
# TODO: Add remaining cases
(
serializers.BooleanField(label=label, help_text=help_text),
coreschema.Boolean(title=label, description=help_text)
),
(
serializers.DecimalField(1000, 1000, label=label, help_text=help_text),
coreschema.Number(title=label, description=help_text)
),
(
serializers.FloatField(label=label, help_text=help_text),
coreschema.Number(title=label, description=help_text)
),
(
serializers.IntegerField(label=label, help_text=help_text),
coreschema.Integer(title=label, description=help_text)
),
(
serializers.DateField(label=label, help_text=help_text),
coreschema.String(title=label, description=help_text, format='date')
),
(
serializers.DateTimeField(label=label, help_text=help_text),
coreschema.String(title=label, description=help_text, format='date-time')
),
(
serializers.JSONField(label=label, help_text=help_text),
coreschema.Object(title=label, description=help_text)
),
]
for case in cases:
self.assertEqual(field_to_schema(case[0]), case[1])
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 get_fields(cls, model):
''' Generate schema fields used to generate API docs. '''
fields = [
coreapi.Field(
name="pedigree_data",
required=True,
location='form',
schema=coreschema.String(
title="Pedigree",
description="CanRisk File Format",
format='textarea',
),
),
coreapi.Field(
name="user_id",
required=True,
location='form',
schema=coreschema.String(
title="User ID",
description="Unique end user ID",
),
),
coreapi.Field(
name="cancer_rates",
required=True,
location='form',
schema=coreschema.Enum(
list(settings.BC_MODEL['CANCER_RATES'].keys()),
title="Cancer rates",
description="Cancer incidence rates",
default="UK",
),
),
coreapi.Field(
name="mut_freq",
required=True,
location='form',
schema=coreschema.Enum(
list(settings.BC_MODEL['MUTATION_FREQUENCIES'].keys()),
title="Mutation frequency",
description="Mutation frequency",
default="UK",
),
),
coreapi.Field(
name="prs",
required=False,
location='form',
schema=coreschema.Object(
title="Polygenic risk score",
description='PRS, e.g. {"alpha":0.45,"zscore":2.652}',
properties={
'alpha': coreschema.Number,
'zscore': coreschema.Number
},
),
),
# coreapi.Field(
# name="risk_factor_code",
# required=False,
# location='form',
# schema=coreschema.Integer(
# minimum=0,
# description="Risk factor code",
# ),
# ),
]
fields += [
coreapi.Field(
name=g.lower() + "_mut_frequency",
required=False,
location='form',
schema=coreschema.Number(title=g + " mutation frequency",
description=g + ' mutation frequency',
minimum=settings.MIN_MUTATION_FREQ,
maximum=settings.MAX_MUTATION_FREQ),
) for g in model['GENES']
]
fields += [
coreapi.Field(
name=g.lower() + "_mut_sensitivity",
required=False,
location='form',
schema=coreschema.Number(
title=g + " mutation sensitivity",
description=g + ' mutation sensitivity',
maximum=1,
),
) for g in model['GENES']
]
return fields
class Zscore2PercentView(APIView):
renderer_classes = (
JSONRenderer,
BrowsableAPIRenderer,
)
serializer_class = ZscoreInputSerializer
authentication_classes = (
SessionAuthentication,
BasicAuthentication,
TokenAuthentication,
)
permission_classes = (IsAuthenticated, )
throttle_classes = (BurstRateThrottle, SustainedRateThrottle,
EndUserIDRateThrottle)
if coreapi is not None and coreschema is not None:
schema = ManualSchema(fields=[
coreapi.Field(
name="sample_name",
required=True,
location='form',
schema=coreschema.Number(
title="z-score",
description="Standard normal PRS",
),
),
],
encoding="application/json",
description="""
Returns PRS represented as a percentage of those with a lower PRS.
""")
def post(self, request):
"""
Returns PRS represented as a percentage of those with a lower PRS.
---
response_serializer: Vcf2PrsOutputSerializer
parameters:
- name: z-score
description: Standard normal PRS
type: number
required: true
responseMessages:
- code: 401
message: Not authenticated
consumes:
- application/json
- application/xml
produces: ['application/json', 'application/xml']
"""
serializer = self.serializer_class(data=request.data)
if serializer.is_valid(raise_exception=True):
zscore = serializer.validated_data.get("zscore")
return Response(
ZscoreOutputSerializer({
"percent":
Zscore2PercentView.get_percentage(zscore)
}).data)
return Response(serializer.errors, status=status.HTTP_400_BAD_REQUEST)
@classmethod
def get_percentage(cls, load):
"""
Use error function to compute cumulative standard normal distribution,
https://docs.python.org/3/library/math.html#math.erf
(alternative to scipy.stats.norm.cdf(load, mu, sigma) * 100.0) to get
percentage representation.
@param: standard normal PRS which is normally distributed in the general population with mean
of 0 and standard deviation of 1
@return: PRS represented as a percentage of those with a lower PRS
"""
return ((1.0 + erf(load / sqrt(2.0))) / 2.0) * 100.0
class CreateQuizAPIView(generics.CreateAPIView):
if coreapi_schema.is_enabled():
schema = ManualSchema(
fields=[
coreapi.Field(
name="title",
required=True,
location='form',
schema=coreschema.String(
title="Title",
description="name of a quiz",
),
),
coreapi.Field(
name="quiz_type",
required=True,
location='form',
schema=coreschema.String(
title="Type of a quiz",
description="Type of a quiz",
),
),
coreapi.Field(
name="timestamp",
required=True,
location='form',
schema=coreschema.Integer(
title="Timestamp",
description="timestamp",
),
),
coreapi.Field(
name="goal",
required=True,
location='form',
schema=coreschema.Integer(
title="Goal",
description="goal for the users",
),
),
coreapi.Field(
name="indicator_value",
required=True,
location='form',
schema=coreschema.Number(
title="Indicator value",
description="indicator value",
),
),
coreapi.Field(
name="author",
required=True,
location='form',
schema=coreschema.String(
title="Author username",
description="author username",
),
),
coreapi.Field(
name="description",
required=True,
location='form',
schema=coreschema.String(
title="question description",
description="description",
),
),
coreapi.Field(
name="vote_detail",
required=True,
location='form',
schema=coreschema.Object(
title="Vote detail",
description="vote details in json format",
),
),
],
encoding="application/json",
)
permission_classes = (permissions.AllowAny, )
serializer_class = serializers.QuizSerializer
queryset = models.Vote.objects.all()
