def getVariants(self,
referenceName,
startPosition,
endPosition,
callSetIds=None):
"""
Returns an iterator over the specified variants. The parameters
correspond to the attributes of a GASearchVariantsRequest object.
"""
if callSetIds is None:
callSetIds = self._callSetIds
else:
for callSetId in callSetIds:
if callSetId not in self._callSetIds:
raise exceptions.CallSetNotInVariantSetException(
callSetId, self.getId())
if referenceName in self._chromFileMap:
varFileName = self._chromFileMap[referenceName]
referenceName, startPosition, endPosition = \
self.sanitizeVariantFileFetch(
referenceName, startPosition, endPosition)
cursor = self.getFileHandle(varFileName).fetch(
referenceName, startPosition, endPosition)
for record in cursor:
yield self.convertVariant(record, callSetIds)
def testCallSetNotInVariantSetException(self):
exception = exceptions.CallSetNotInVariantSetException('csId', 'vsId')
response = frontend.handleException(exception)
self.assertEquals(response.status_code, 404)
gaException = self.getGa4ghException(response.data)
self.assertGreater(len(gaException.message), 0)
self.assertFalse(frontend.app.log_exception.called)
def getVariants(self, referenceName, startPosition, endPosition,
variantName=None, callSetIds=None):
"""
Returns an iterator over the specified variants. The parameters
correspond to the attributes of a GASearchVariantsRequest object.
"""
if variantName is not None:
raise exceptions.NotImplementedException(
"Searching by variantName is not supported")
# For v0.5.1, callSetIds=[] actually means return all callSets.
# In v0.6+, callSetIds=[] means return no call sets, and
# callSetIds=None means return all call sets. For forward
# compatibility, we use the 0.6 interface for this function but
# we translate back to the 0.5 interface while we support this.
# TODO Remove this comment and workaround once we transition to
# protocol version 0.6
if callSetIds is None:
callSetIds = []
else:
for callSetId in callSetIds:
if callSetId not in self._callSetIds:
raise exceptions.CallSetNotInVariantSetException(
callSetId, self.getId())
if len(callSetIds) == 0:
callSetIds = self._callSetIds
if referenceName in self._chromFileMap:
varFileName = self._chromFileMap[referenceName]
referenceName, startPosition, endPosition = \
self.sanitizeVariantFileFetch(
referenceName, startPosition, endPosition)
cursor = self.getFileHandle(varFileName).fetch(
referenceName, startPosition, endPosition)
for record in cursor:
yield self.convertVariant(record, callSetIds)
