def runSearchRequest(self, requestStr, requestClass, responseClass,
objectGenerator):
"""
Runs the specified request. The request is a string containing
a JSON representation of an instance of the specified requestClass.
We return a string representation of an instance of the specified
responseClass in JSON format. Objects are filled into the page list
using the specified object generator, which must return
(object, nextPageToken) pairs, and be able to resume iteration from
any point using the nextPageToken attribute of the request object.
"""
self.startProfile()
try:
request = protocol.fromJson(requestStr, requestClass)
except protocol.json_format.ParseError:
raise exceptions.InvalidJsonException(requestStr)
# TODO How do we detect when the page size is not set?
if not request.page_size:
request.page_size = self._defaultPageSize
if request.page_size < 0:
raise exceptions.BadPageSizeException(request.page_size)
responseBuilder = protocol.SearchResponseBuilder(
responseClass, request.page_size, self._maxResponseLength)
nextPageToken = None
for obj, nextPageToken in objectGenerator(request):
responseBuilder.addValue(obj)
if responseBuilder.isFull():
break
responseBuilder.setNextPageToken(nextPageToken)
responseString = responseBuilder.getSerializedResponse()
self.endProfile()
return responseString
def populateFromJson(self, jsonString):
try:
parsed = protocol.fromJson(jsonString, protocol.BioSample)
except:
raise exceptions.InvalidJsonException(jsonString)
self._created = parsed.created
self._updated = parsed.updated
self._description = parsed.description
self._disease = protocol.toJsonDict(parsed.disease)
self._individualId = parsed.individual_id
self._info = {}
for key in parsed.info:
self._info[key] = {"values": protocol.toJsonDict(parsed.info[key])}
return self
def populateFromJson(self, jsonString):
# TODO validate
try:
parsed = protocol.fromJson(jsonString, protocol.Individual)
except:
raise exceptions.InvalidJsonException(jsonString)
self._created = parsed.created
self._updated = parsed.updated
self._description = parsed.description
self._species = protocol.toJsonDict(parsed.species)
self._sex = protocol.toJsonDict(parsed.sex)
self._info = {}
for key in parsed.info:
self._info[key] = {"values": protocol.toJsonDict(parsed.info[key])}
return self
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)
