def sendReferenceBasesList(self, id_=None):
if id_ is None:
id_ = self.referenceId
path = "/references/{}/bases".format(id_)
request = protocol.ListReferenceBasesRequest()
response = self.sendListRequest(path, request)
return response
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)
def post(self, url, params=None, data=None):
self.checkSessionParameters()
assert url.startswith(self._urlPrefix)
suffix = url[len(self._urlPrefix):]
searchSuffix = "/search"
if suffix.endswith(searchSuffix):
datatype = suffix[1:-len(searchSuffix)]
assert datatype in self._searchMethodMap
method = self._searchMethodMap[datatype]
result = method(data)
else:
# ListReferenceBases is an oddball and needs to be treated
# separately.
data = json.loads(data)
args = protocol.ListReferenceBasesRequest()
args.reference_id = data.get('referenceId', "")
args.start = int(data.get('start', 0))
args.end = int(data.get('end', 0))
args.page_token = data.get('pageToken', "")
result = self._backend.runListReferenceBases(protocol.toJson(args))
return DummyResponse(result)
def list_reference_bases(self, id_, start=0, end=None):
"""
Returns an iterator over the bases from the server in the form
of consecutive strings. This command does not conform to the
patterns of the other search and get requests, and is implemented
differently.
"""
request = protocol.ListReferenceBasesRequest()
request.start = pb.int(start)
request.end = pb.int(end)
request.reference_id = id_
not_done = True
# TODO We should probably use a StringIO here to make string buffering
# a bit more efficient.
bases_list = []
while not_done:
response = self._run_list_reference_bases_page_request(request)
bases_list.append(response.sequence)
not_done = bool(response.next_page_token)
request.page_token = response.next_page_token
return "".join(bases_list)