class MAFRecord(Message):
sample_id = StringField(1)
patient_id = StringField(2)
aliquot_id = StringField(3)
hugo_symbol = StringField(4)
uniprot_aapos = IntegerField(5, variant=Variant.INT32)
uniprot_id = StringField(6)
variant_classification = StringField(7)
cohort = IntegerField(8, repeated=True)
class MAFRecordList(Message):
items = MessageField(MAFRecord, 1, repeated=True)
cohort_set = MessageField(PlotDataCohortInfo, 2, repeated=True)
SeqPeekDataEndpointsAPI = endpoints_api(name='seqpeek_data_api', version='v1',
description='Endpoints used by the seqpeek visualization in the web application.')
def maf_array_to_record(maf_array):
data_points = []
for item in maf_array:
data_points.append(MAFRecord(**item))
return data_points
@SeqPeekDataEndpointsAPI.api_class(resource_name='data_endpoints')
class SeqPeekDataAccessAPI(remote.Service):
def create_response(self, maf_with_cohorts):
num_patients_wo_y = IntegerField(7, required=True)
num_samples_wo_y = IntegerField(8, required=True)
class PlotDataResponse(Message):
types = MessageField(PlotDataTypes, 1, required=True)
labels = MessageField(PlotDataFeatureLabels, 2, required=True)
items = MessageField(PlotDataPoint, 3, repeated=True)
cohort_set = MessageField(PlotDataCohortInfo, 4, repeated=True)
counts = MessageField(PlotDatapointCount, 5)
pairwise_result = MessageField(PairwiseResults, 6, required=False)
xUnits = StringField(7, required=False)
yUnits = StringField(8, required=False)
FeatureDataEndpointsAPI = endpoints_api(name='feature_data_api', version='v1',
description='Endpoints for feature data used by the web application.')
@FeatureDataEndpointsAPI.api_class(resource_name='feature_data_endpoints')
class FeatureDataEndpoints(remote.Service):
def get_counts(self, data):
total_num_patients = []
total_num_samples = []
num_samples_w_xy = []
num_patients_w_xy = []
num_samples_wo_x = []
num_samples_wo_y = []
num_patients_wo_x = []
num_patients_wo_y = []
result = {}
elif datatype == METH_FEATURE_TYPE:
return METHSearcher()
elif datatype == CNVR_FEATURE_TYPE:
return CNVRSearcher()
elif datatype == RPPA_FEATURE_TYPE:
return RPPASearcher()
elif datatype == MIRN_FEATURE_TYPE:
return MIRNSearcher()
elif datatype == GNAB_FEATURE_TYPE:
return GNABSearcher()
#TODO build a full search on all features
#elif datatype == ALL:
# return FullSearcher()
raise InvalidDataTypeException("Invalid datatype '{datatype}'".format(datatype=datatype))
FeatureAccessEndpointsAPI = endpoints_api(name='feature_type_api', version='v1',
description='Endpoints used by the web application to return features.')
@FeatureAccessEndpointsAPI.api_class(resource_name='feature_type_endpoints')
class FeatureAccessEndpoints(remote.Service):
@endpoints_method(FeatureTypeSearchRequest, FeatureTypeList,
path='feature_search', http_method='GET', name='feature_access.FeatureSearch')
def feature_search(self, request):
""" Used by the web application."""
try:
datatype = request.datatype
searcher = FeatureDefinitionSearcherFactory.build_from_datatype(datatype)
parameters = {}
for message in request.all_fields():
field_name = message.name
if field_name != 'datatype':
value = request.get_assigned_value(field_name)
if value is not None:
