def runListReferenceBases(self, id_, requestArgs):
"""
Runs a listReferenceBases request for the specified ID and
request arguments.
"""
compoundId = datamodel.ReferenceCompoundId.parse(id_)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(id_)
start = _parseIntegerArgument(requestArgs, 'start', 0)
end = _parseIntegerArgument(requestArgs, 'end', reference.getLength())
if end == 0: # assume meant "get all"
end = reference.getLength()
if 'pageToken' in requestArgs:
pageTokenStr = requestArgs['pageToken']
if pageTokenStr != "":
start = _parsePageToken(pageTokenStr, 1)[0]
chunkSize = self._maxResponseLength
nextPageToken = None
if start + chunkSize < end:
end = start + chunkSize
nextPageToken = str(start + chunkSize)
sequence = reference.getBases(start, end)
# build response
response = protocol.ListReferenceBasesResponse()
response.offset = start
response.sequence = sequence
if nextPageToken is not None:
response.next_page_token = nextPageToken
return protocol.toJson(response)
def runListReferenceBases(self, id_, requestArgs):
"""
Runs a listReferenceBases request for the specified ID and
request arguments.
"""
compoundId = datamodel.ReferenceCompoundId.parse(id_)
referenceSet = self.getReferenceSet(compoundId.referenceSetId)
reference = referenceSet.getReference(id_)
start = _parseIntegerArgument(requestArgs, 'start', 0)
end = _parseIntegerArgument(requestArgs, 'end', reference.getLength())
if 'pageToken' in requestArgs:
pageTokenStr = requestArgs['pageToken']
start = _parsePageToken(pageTokenStr, 1)[0]
chunkSize = self._maxResponseLength
nextPageToken = None
if start + chunkSize < end:
end = start + chunkSize
nextPageToken = str(start + chunkSize)
sequence = reference.getBases(start, end)
# build response
response = protocol.ListReferenceBasesResponse()
response.offset = start
response.sequence = sequence
response.nextPageToken = nextPageToken
return response.toJsonString()
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 runListReferenceBases(self, requestJson):
"""
Runs a listReferenceBases request for the specified ID and
request arguments.
"""
# In the case when an empty post request is made to the endpoint
# we instantiate an empty ListReferenceBasesRequest.
if not requestJson:
request = protocol.ListReferenceBasesRequest()
else:
try:
request = protocol.fromJson(requestJson,
protocol.ListReferenceBasesRequest)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestJson)
compoundId = datamodel.ReferenceCompoundId.parse(request.reference_id)
referenceSet = self.getDataRepository().getReferenceSet(
compoundId.reference_set_id)
reference = referenceSet.getReference(request.reference_id)
start = request.start
end = request.end
if end == 0: # assume meant "get all"
end = reference.getLength()
if request.page_token:
pageTokenStr = request.page_token
start = paging._parsePageToken(pageTokenStr, 1)[0]
chunkSize = self._maxResponseLength
nextPageToken = None
if start + chunkSize < end:
end = start + chunkSize
nextPageToken = str(start + chunkSize)
sequence = reference.getBases(start, end)
# build response
response = protocol.ListReferenceBasesResponse()
response.offset = start
response.sequence = sequence
if nextPageToken:
response.next_page_token = nextPageToken
return protocol.toJson(response)