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()