def testAddOneReference(self):
self.assertEqual(self._referenceSet.getNumReferences(), 0)
referenceName = "ref"
reference = references.AbstractReference(self._referenceSet,
referenceName)
self._referenceSet.addReference(reference)
self.assertEqual(self._referenceSet.getNumReferences(), 1)
self.assertEqual(self._referenceSet.getReferenceByIndex(0), reference)
self.assertEqual(self._referenceSet.getReferenceByName(referenceName),
reference)
self.assertEqual(self._referenceSet.getReference(reference.getId()),
reference)
self.assertEqual(self._referenceSet.getReferences(), [reference])
def testListReferenceBasesErrors(self):
referenceSet = self.backend.getReferenceSets()[0]
for badId in self.getBadIds():
path = '/references/{}/bases'.format(badId)
response = self.app.get(path)
self.assertEqual(response.status_code, 404)
reference = references.AbstractReference(referenceSet, badId)
path = '/references/{}/bases'.format(reference.getId())
response = self.app.get(path)
self.assertEqual(response.status_code, 404)
reference = referenceSet.getReferences()[0]
path = '/references/{}/bases'.format(reference.getId())
length = reference.getLength()
badRanges = [(-1, 0), (-1, -1), (length, 0), (0, length + 1)]
for start, end in badRanges:
args = protocol.ListReferenceBasesRequest()
args.start, args.end = start, end
response = self.app.get(path, query_string=args.toJsonDict())
self.assertEqual(response.status_code, 416)
def testAddMultipleReference(self):
referenceList = []
referenceBaseName = "ref"
referenceCount = 10
self.assertEqual(self._referenceSet.getNumReferences(), 0)
for i in range(referenceCount):
referenceName = referenceBaseName + str(i)
reference = references.AbstractReference(self._referenceSet,
referenceName)
referenceList.append(reference)
self._referenceSet.addReference(reference)
self.assertEqual(self._referenceSet.getNumReferences(), i + 1)
self.assertEqual(self._referenceSet.getReferenceByIndex(i),
reference)
self.assertEqual(
self._referenceSet.getReferenceByName(referenceName),
reference)
self.assertEqual(
self._referenceSet.getReference(reference.getId()), reference)
self.assertEqual(self._referenceSet.getReferences(), referenceList)
def setUp(self):
self._backend = backend.Backend(datarepo.AbstractDataRepository())
self._referenceSet = references.AbstractReferenceSet(self._backend)
self._reference = references.AbstractReference(self._referenceSet,
"ref")
def _addReference(self, referenceName):
reference = references.AbstractReference(self._referenceSet,
referenceName)
self._referenceSet.addReference(reference)
def setUp(self):
self._backend = backend.AbstractBackend()
self._referenceSet = references.AbstractReferenceSet(self._backend)
self._reference = references.AbstractReference(self._referenceSet,
"ref")