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_schema_fields(self, view):
assert coreapi is not None, 'coreapi must be installed to use `get_schema_fields()`'
assert coreschema is not None, 'coreschema must be installed to use `get_schema_fields()`'
# display aliases
ordering_choices = [
fields[0] for fields in super().get_valid_fields(None, view)
]
return [
coreapi.Field(name=self.ordering_param,
required=False,
location='query',
schema=coreschema.Enum(
title=force_str(self.ordering_title),
enum=ordering_choices,
description=force_str(
self.ordering_description)))
]
def format_field(self, value):
dic = {"type": ""}
error_messages = value.error_messages
description = ""
if isinstance(value, CharField):
max_length = value.max_length
min_length = value.min_length
if max_length:
description += "max_length is %d " % max_length
if min_length:
description += "min_length is %d " % min_length
dic["type"] = "string"
dic["schema"] = coreschema.String(title='',
description=description,
min_length=min_length,
max_length=max_length)
elif isinstance(value, IntegerField):
min_value = value.min_value
max_value = value.max_value
if max_value:
description += "max_value is %d " % max_value
if min_value:
description += "min_value is %d " % min_value
dic["schema"] = coreschema.Integer(title='',
description=description,
minimum=min_value,
maximum=max_value)
dic["type"] = "integer"
elif isinstance(value, ChoiceField):
choices = value._choices
description += str(choices).strip('[]')
choice_list = set([k[0] for k in choices])
dic["type"] = "enum"
dic["schema"] = coreschema.Enum(title='',
description=description,
enum=choice_list)
else:
dic["type"] = "string"
dic["schema"] = coreschema.String(title='',
description=description)
dic["description"] = description + value.help_text
return dic
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 Vcf2PrsView(APIView):
renderer_classes = (
JSONRenderer,
BrowsableAPIRenderer,
)
serializer_class = Vcf2PrsInputSerializer
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="vcf_file",
required=True,
location='form',
schema=coreschema.String(
title="VCF",
description="VCF File Format",
format='textarea',
),
),
coreapi.Field(
name="sample_name",
required=True,
location='form',
schema=coreschema.String(
title="Sample Name",
description="Sample Name",
),
),
coreapi.Field(
name="bc_prs_reference_file",
location='form',
schema=coreschema.Enum(
list(settings.BC_MODEL['PRS_REFERENCE_FILES'].values()),
title="Breast cancer PRS reference file",
description="Breast cancer PRS reference file",
default=None,
),
),
coreapi.Field(
name="oc_prs_reference_file",
location='form',
schema=coreschema.Enum(
list(settings.OC_MODEL['PRS_REFERENCE_FILES'].values()),
title="Ovarian cancer PRS reference file",
description="Ovarian cancer PRS reference file",
default=None,
),
),
],
encoding="application/json",
description="""
Variant Call Format (VCF) file to Polygenic Risk Score (PRS) web-service.
""")
def post(self, request):
"""
Calculate PRS from a vcf file.
---
response_serializer: Vcf2PrsOutputSerializer
parameters:
- name: sample_name
description: name of the sample in the genotype file to be used to calculate the PRS
type: string
required: true
- name: vcf_file
description: VCF genotype file
type: file
required: true
responseMessages:
- code: 401
message: Not authenticated
consumes:
- application/json
- application/xml
produces: ['application/json', 'application/xml']
"""
start = time.time()
serializer = self.serializer_class(data=request.data)
if serializer.is_valid(raise_exception=True):
validated_data = serializer.validated_data
vcf_file = validated_data.get("vcf_file")
vcf_stream = io.StringIO(vcf_file)
moduledir = Path(vcf2prs.__file__).parent.parent
bc_prs_ref_file = validated_data.get("bc_prs_reference_file", None)
oc_prs_ref_file = validated_data.get("oc_prs_reference_file", None)
if bc_prs_ref_file is None and oc_prs_ref_file is None:
raise ValidationError(
'No breast or ovarian cancer PRS reference file provided')
else:
if bc_prs_ref_file is not None:
bc_prs_ref_file = os.path.join(moduledir, "PRS_files",
bc_prs_ref_file)
if oc_prs_ref_file is not None:
oc_prs_ref_file = os.path.join(moduledir, "PRS_files",
oc_prs_ref_file)
sample_name = validated_data.get("sample_name", None)
try:
if bc_prs_ref_file is not None:
breast_prs = Prs(prs_file=bc_prs_ref_file,
geno_file=vcf_stream,
sample=sample_name)
bc_alpha = breast_prs.alpha
bc_zscore = breast_prs.z_Score
else:
bc_alpha = 0
bc_zscore = 0
if oc_prs_ref_file is not None:
ovarian_prs = Prs(prs_file=oc_prs_ref_file,
geno_content=vcf_stream,
sample=sample_name)
oc_alpha = ovarian_prs.alpha
oc_zscore = ovarian_prs.z_Score
else:
oc_alpha = 0
oc_zscore = 0
data = {
'breast_cancer_prs': {
'alpha': bc_alpha,
'zscore': bc_zscore,
'percent': Zscore2PercentView.get_percentage(bc_zscore)
},
'ovarian_cancer_prs': {
'alpha': oc_alpha,
'zscore': oc_zscore,
'percent': Zscore2PercentView.get_percentage(oc_zscore)
}
}
prs_serializer = Vcf2PrsOutputSerializer(data)
logger.info("PRS elapsed time=" + str(time.time() - start))
return Response(prs_serializer.data)
except Vcf2PrsError as ex:
logger.debug(ex)
data = {
'error': str(ex),
'samples': self.get_samples(vcf_file)
}
raise NotAcceptable(data)
return Response(serializer.errors, status=status.HTTP_400_BAD_REQUEST)
def get_samples(self, vcf_file):
""" Get the samples in the VCF file. """
try:
fsock = io.StringIO(vcf_file)
vcf_content = vcf.Reader(fsock)
samples = vcf_content.samples
fsock.close()
return samples
except Exception:
logging.warn(traceback.format_exc())
status=status.HTTP_404_NOT_FOUND)
return Response(status=status.HTTP_405_METHOD_NOT_ALLOWED)
@api_view(['PATCH'])
@authentication_classes((OAuth2Authentication, BasicAuthentication))
@permission_classes((IsAuthenticated, HasApiPermission))
@schema(
MethodSchema(
manual_fields={
'PATCH': [
coreapi.Field(
name='op',
location='form',
required=True,
schema=coreschema.Enum(
enum=['start', 'reboot', 'shutdown', 'poweroff'])),
],
}))
def vm_operations(request, vm_id, format=None):
if request.method == 'PATCH':
args = {
'req_user': request.user,
'uuid': vm_id,
'op': request.data.get('op'),
}
print(args)
dic = api_vm_op(args)
if dic['res']:
return Response(status=status.HTTP_201_CREATED)
if dic['err'] == ERR_AUTH_PERM:
