def readsGenerator(self, request):
"""
Returns a generator over the (read, nextPageToken) pairs defined
by the specified request
"""
if not request.reference_id:
raise exceptions.UnmappedReadsNotSupported()
if len(request.read_group_ids) < 1:
raise exceptions.BadRequestException(
"At least one readGroupId must be specified")
elif len(request.read_group_ids) == 1:
return self._readsGeneratorSingle(request)
else:
return self._readsGeneratorMultiple(request)
def _readsGeneratorMultiple(self, request):
compoundId = datamodel.ReadGroupCompoundId.parse(
request.read_group_ids[0])
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
referenceSet = readGroupSet.getReferenceSet()
if referenceSet is None:
raise exceptions.ReadGroupSetNotMappedToReferenceSetException(
readGroupSet.getId())
reference = referenceSet.getReference(request.reference_id)
readGroupIds = readGroupSet.getReadGroupIds()
if set(readGroupIds) != set(request.read_group_ids):
raise exceptions.BadRequestException(
"If multiple readGroupIds are specified, "
"they must be all of the readGroupIds in a ReadGroupSet")
intervalIterator = paging.ReadsIntervalIterator(
request, readGroupSet, reference)
return intervalIterator
def runAddAnnouncement(self, flaskrequest):
"""
Takes a flask request from the frontend and attempts to parse
into an AnnouncePeerRequest. If successful, it will log the
announcement to the `announcement` table with some other metadata
gathered from the request.
"""
announcement = {}
# We want to parse the request ourselves to collect a little more
# data about it.
try:
requestData = protocol.fromJson(
flaskrequest.get_data(), protocol.AnnouncePeerRequest)
announcement['hostname'] = flaskrequest.host_url
announcement['remote_addr'] = flaskrequest.remote_addr
announcement['user_agent'] = flaskrequest.headers.get('User-Agent')
except AttributeError:
# Sometimes in testing we will send protocol requests instead
# of flask requests and so the hostname and user agent won't
# be present.
try:
requestData = protocol.fromJson(
flaskrequest, protocol.AnnouncePeerRequest)
except Exception as e:
raise exceptions.InvalidJsonException(e)
except Exception as e:
raise exceptions.InvalidJsonException(e)
# Validate the url before accepting the announcement
peer = datamodel.peers.Peer(requestData.peer.url)
peer.setAttributesJson(protocol.toJson(
requestData.peer.attributes))
announcement['url'] = peer.getUrl()
announcement['attributes'] = peer.getAttributes()
try:
self.getDataRepository().insertAnnouncement(announcement)
except:
raise exceptions.BadRequestException(announcement['url'])
return protocol.toJson(
protocol.AnnouncePeerResponse(success=True))
def rnaQuantificationsGenerator(self, request):
"""
Returns a generator over the (rnaQuantification, nextPageToken) pairs
defined by the specified request.
"""
if len(request.rna_quantification_set_id) < 1:
raise exceptions.BadRequestException(
"Rna Quantification Set Id must be specified")
else:
compoundId = datamodel.RnaQuantificationSetCompoundId.parse(
request.rna_quantification_set_id)
dataset = self.getDataRepository().getDataset(
compoundId.dataset_id)
rnaQuantSet = dataset.getRnaQuantificationSet(
compoundId.rna_quantification_set_id)
results = []
for obj in rnaQuantSet.getRnaQuantifications():
include = True
if request.biosample_id:
if request.biosample_id != obj.getBiosampleId():
include = False
if include:
results.append(obj)
return self._objectListGenerator(request, results)
