def _readGroupSetsGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, which
is over a set of objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(request.page_token, 1)
while currentIndex < numObjects:
obj = getByIndexMethod(currentIndex)
include = True
rgsp = obj.toProtocolElement()
if request.name and request.name != obj.getLocalId():
include = False
if request.bio_sample_id and include:
rgsp.ClearField("read_groups")
for readGroup in obj.getReadGroups():
if request.bio_sample_id == readGroup.getBioSampleId():
rgsp.read_groups.extend(
[readGroup.toProtocolElement()])
# If none of the biosamples match and the readgroupset
# contains reagroups, don't include in the response
if len(rgsp.read_groups) == 0 and \
len(obj.getReadGroups()) != 0:
include = False
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
if include:
yield rgsp, nextPageToken
def _topLevelObjectGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, which
is over a set of objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(request.page_token, 1)
while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
yield object_.toProtocolElement(), nextPageToken
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 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 _topLevelObjectGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, which
is over a set of objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
object_ = getByIndexMethod(currentIndex)
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
yield object_.toProtocolElement(), nextPageToken
def _readGroupSetsGenerator(self, request, numObjects, getByIndexMethod):
"""
Returns a generator over the results for the specified request, which
is over a set of objects of the specified size. The objects are
returned by call to the specified method, which must take a single
integer as an argument. The returned generator yields a sequence of
(object, nextPageToken) pairs, which allows this iteration to be picked
up at any point.
"""
currentIndex = 0
if request.page_token:
currentIndex, = paging._parsePageToken(
request.page_token, 1)
while currentIndex < numObjects:
obj = getByIndexMethod(currentIndex)
include = True
rgsp = obj.toProtocolElement()
if request.name and request.name != obj.getLocalId():
include = False
if request.biosample_id and include:
rgsp.ClearField("read_groups")
for readGroup in obj.getReadGroups():
if request.biosample_id == readGroup.getBiosampleId():
rgsp.read_groups.extend(
[readGroup.toProtocolElement()])
# If none of the biosamples match and the readgroupset
# contains reagroups, don't include in the response
if len(rgsp.read_groups) == 0 and \
len(obj.getReadGroups()) != 0:
include = False
currentIndex += 1
nextPageToken = None
if currentIndex < numObjects:
nextPageToken = str(currentIndex)
if include:
yield rgsp, nextPageToken
def testParsePageToken(self):
goodPageToken = "12:34:567:8:9000"
parsedToken = paging._parsePageToken(goodPageToken, 5)
self.assertEqual(parsedToken[2], 567)
def testParsePageToken(self):
goodPageToken = "12:34:567:8:9000"
parsedToken = paging._parsePageToken(goodPageToken, 5)
self.assertEqual(parsedToken[2], 567)