def setUp(self):
self._backend = backend.Backend(
datarepo.AbstractDataRepository())
self._referenceSet = references.AbstractReferenceSet(
'refSetId')
self._reference = references.AbstractReference(
self._referenceSet, "ref")
def __init__(self, localId, dataPath):
self._backend = backend.Backend(datarepo.AbstractDataRepository())
self._referenceSet = None
self._dataset = datasets.Dataset("ds")
self._readGroupInfos = {}
self._readGroupSetInfo = None
self._samFile = pysam.AlignmentFile(dataPath)
self._readReferences()
super(ReadGroupSetTest, self).__init__(localId, dataPath)
self._readAlignmentInfo()
def setUp(self):
class FakeRequest(object):
pass
class FakeTopLevelObject(object):
def toProtocolElement(self, tier=0):
return self
self.request = FakeRequest()
self.request.page_token = ""
self.num_objects = 3
self.objects = [FakeTopLevelObject() for j in range(self.num_objects)]
self.backend = backend.Backend(datarepo.AbstractDataRepository())
def setUp(self):
self._backend = backend.Backend(datarepo.AbstractDataRepository())
self._dataRepo = self._backend.getDataRepository()