def runListReferenceBases(self, id_, requestArgs):
"""
Runs a listReferenceBases request for the specified ID and
request arguments.
"""
# parse arguments
reference = _safeMapQuery(self._referenceIdMap, id_,
exceptions.ObjectWithIdNotFoundException)
start = 0
end = datamodel.PysamDatamodelMixin.fastaMax
if 'start' in requestArgs:
startString = requestArgs['start']
try:
start = int(startString)
except ValueError:
raise exceptions.BadRequestIntegerException(
'start', startString)
if 'end' in requestArgs:
endString = requestArgs['end']
try:
end = int(endString)
except ValueError:
raise exceptions.BadRequestIntegerException('end', endString)
if 'pageToken' in requestArgs:
pageTokenStr = requestArgs['pageToken']
start = _parsePageToken(pageTokenStr, 1)[0]
chunkSize = self._maxResponseLength
# get reference bases
gbEnd = min(start + chunkSize, end)
sequence = reference.getBases(start, gbEnd)
# determine nextPageToken
if len(sequence) == chunkSize:
nextPageToken = start + chunkSize
elif len(sequence) > chunkSize:
raise exceptions.ServerError() # should never happen
else:
nextPageToken = None
# build response
response = protocol.ListReferenceBasesResponse()
response.offset = start
response.sequence = sequence
response.nextPageToken = nextPageToken
return response.toJsonString()
def _parseIntegerArgument(args, key, defaultValue):
"""
Attempts to parse the specified key in the specified argument
dictionary into an integer. If the argument cannot be parsed,
raises a BadRequestIntegerException. If the key is not present,
return the specified default value.
"""
ret = defaultValue
if key in args:
try:
ret = int(args[key])
except ValueError:
raise exceptions.BadRequestIntegerException(key, args[key])
return ret
