def testFindMatchAfterSaveRestore(self):
"""
A matching subject found before a save/restore must also be found
following a database save/restore.
"""
subject = AARead('subject', 'AFRRRFRRRFASAASAVVVVVVASAVVVASA')
query = AARead('query', 'FRRRFRRRFASAASAFRRRFRRRFFRRRFRRRFFRRRFRRRF')
dbParams = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks])
db1 = Database(dbParams)
db1.addSubject(subject)
result = db1.find(query)
expected = {
'0': [{
'queryLandmark': Landmark('AlphaHelix', 'A', 0, 9, 2),
'queryTrigPoint': TrigPoint('Peaks', 'P', 10),
'subjectLandmark': Landmark('AlphaHelix', 'A', 1, 9, 2),
'subjectTrigPoint': TrigPoint('Peaks', 'P', 11),
}, {
'queryLandmark': Landmark('AlphaHelix', 'A', 0, 9, 2),
'queryTrigPoint': TrigPoint('Peaks', 'P', 13),
'subjectLandmark': Landmark('AlphaHelix', 'A', 1, 9, 2),
'subjectTrigPoint': TrigPoint('Peaks', 'P', 14),
}]
}
self.assertEqual(expected, result.matches)
fp = StringIO()
db1.save(fp)
fp.seek(0)
db2 = Database.restore(fp)
result = db2.find(query)
self.assertEqual(expected, result.matches)
def testChecksumAfterSaveRestore(self):
"""
A database 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 database that simply has the two sequences added to
it without the intervening save/restore.
"""
seq1 = 'FRRRFRRRFASAASA'
seq2 = 'MMMMMMMMMFRRRFR'
dbParams1 = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs])
db1 = Database(dbParams1)
db1.addSubject(AARead('id1', seq1))
fp = StringIO()
db1.save(fp)
fp.seek(0)
db1 = Database.restore(fp)
db1.addSubject(AARead('id2', seq2))
dbParams2 = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs])
db2 = Database(dbParams2)
db2.addSubject(AARead('id1', seq1))
db2.addSubject(AARead('id2', seq2))
self.assertEqual(db1.checksum(), db2.checksum())
def testSaveRestoreEmpty(self):
"""
When asked to save and then restore an empty database, the correct
database must result.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix],
trigPoints=[Peaks])
db = Database(dbParams)
fp = StringIO()
db.save(fp)
fp.seek(0)
result = db.restore(fp)
self.assertEqual(0, result.subjectCount())
self.assertEqual(0, result.totalCoveredResidues())
self.assertEqual(0, result.totalResidues())
self.assertIs(None, dbParams.compare(result.dbParams))
def testSaveRestoreWithNonDefaultParameters(self):
"""
When asked to save and then restore a database with non-default
parameters, a database with the correct parameters must result.
"""
dbParams = DatabaseParameters(landmarks=[],
trigPoints=[],
limitPerLandmark=16,
maxDistance=17,
minDistance=18,
distanceBase=19.0)
db = Database(dbParams)
fp = StringIO()
db.save(fp)
fp.seek(0)
result = db.restore(fp)
self.assertIs(None, dbParams.compare(result.dbParams))
def testSaveContentHasFourParts(self):
"""
When a simple database saves, its content must include parts for the
database parameters, the database state, the backend parameters and
the backend state.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix],
trigPoints=[Peaks])
db = Database(dbParams)
fp = StringIO()
db.save(fp)
fp.seek(0)
dbParams = DatabaseParameters.restore(fp)
loads(fp.readline()[:-1])
backendParams = DatabaseParameters.restore(fp)
loads(fp.readline()[:-1])
self.assertIs(None, dbParams.compare(backendParams))
def testSaveRestoreNonEmpty(self):
"""
When asked to save and then restore a non-empty database, the correct
database must result.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix, BetaStrand],
trigPoints=[Peaks, Troughs])
db = Database(dbParams)
db.addSubject(AARead('id', 'FRRRFRRRFASAASA'))
fp = StringIO()
db.save(fp)
fp.seek(0)
result = db.restore(fp)
self.assertIs(None, dbParams.compare(result.dbParams))
self.assertEqual(db.subjectCount(), result.subjectCount())
self.assertEqual(db.totalCoveredResidues(),
result.totalCoveredResidues())
self.assertEqual(db.totalResidues(), result.totalResidues())
self.assertEqual(db.checksum(), result.checksum())
def testSaveContentIncludesExpectedKeysAndValues(self):
"""
When the database saves, its JSON content must include the expected
keys and values.
"""
dbParams = DatabaseParameters(landmarks=[AlphaHelix],
trigPoints=[Peaks])
db = Database(dbParams)
fp = StringIO()
db.save(fp)
fp.seek(0)
DatabaseParameters.restore(fp)
state = loads(fp.readline()[:-1])
# Keys
self.assertEqual(['_connectorClassName'], list(state.keys()))
# Values
self.assertEqual('SimpleConnector', state['_connectorClassName'])