def testChecksumAfterSaveRestore(self):
"""
A backend that has a sequence added to it, which is then saved and
restored, and then has a second sequence is added to it must have the
same checksum as a backend that simply has the two sequences added to
it without interruption.
"""
seq1 = 'FRRRFRRRFASAASA'
seq2 = 'MMMMMMMMMFRRRFR'
dbParams1 = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs])
be1 = Backend()
be1.configure(dbParams1, 'name1', 0)
be1.addSubject(AARead('id1', seq1), '0')
fp = StringIO()
be1.save(fp)
fp.seek(0)
be1 = Backend.restore(fp)
be1.addSubject(AARead('id2', seq2), '1')
dbParams2 = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs])
be2 = Backend()
be2.configure(dbParams2, 'name2', 0)
be2.addSubject(AARead('id1', seq1), '0')
be2.addSubject(AARead('id2', seq2), '1')
self.assertEqual(be1.checksum(), be2.checksum())
def testSaveContentIncludesExpectedKeysAndValues(self):
"""
When a backend saves, its JSON content must include the expected
keys and values.
"""
dbParams = DatabaseParameters(landmarks=[], trigPoints=[],
limitPerLandmark=16, maxDistance=17,
minDistance=18, distanceBase=19.0)
be = Backend()
be.configure(dbParams, 'backend', 33)
fp = StringIO()
be.save(fp)
fp.seek(0)
DatabaseParameters.restore(fp)
SubjectStore.restore(fp)
state = loads(fp.readline()[:-1])
# Keys
self.assertEqual(
set(['checksum', 'd', 'name', '_totalCoveredResidues']),
set(state.keys()))
# Values
self.assertEqual(be.checksum(), state['checksum'])
self.assertEqual({}, state['d'])
self.assertEqual('backend', state['name'])
self.assertEqual(0, state['_totalCoveredResidues'])
def testInitialChecksum(self):
"""
The backend checksum must be set to the value passed to its
__init__ method.
"""
dbParams = DatabaseParameters(landmarks=[], trigPoints=[])
be = Backend()
be.configure(dbParams, 'backend', 10)
self.assertEqual(10, be.checksum())
def testChecksumAfterSubjectAdded(self):
"""
The backend checksum must be as expected when a subject has been
added to the backend.
"""
dbParams = DatabaseParameters(landmarks=[], trigPoints=[])
be = Backend()
be.configure(dbParams, 'backend', 10)
sequence = 'AFRRRFRRRFASAASA'
subject = AARead('id', sequence)
be.addSubject(subject, '0')
expected = Checksum(10).update([
'id',
sequence,
])
self.assertEqual(expected.value, be.checksum())
def testSaveRestoreNonEmpty(self):
"""
When asked to save and then restore a non-empty backend, the correct
backend must result.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs])
be = Backend()
be.configure(dbParams)
be.addSubject(AARead('id', 'FRRRFRRRFASAASA'), '0')
fp = StringIO()
be.save(fp)
fp.seek(0)
result = Backend.restore(fp)
self.assertEqual(be.subjectCount(), result.subjectCount())
self.assertEqual(be.d, result.d)
self.assertEqual(be.checksum(), result.checksum())
self.assertIs(None, be.dbParams.compare(result.dbParams))
