def testGetReferenceSetByIndexBadIndex(self): self.assertRaises(IndexError, self._dataRepo.getReferenceSetByIndex, 0) self.assertRaises(TypeError, self._dataRepo.getReferenceSetByIndex, None) self.assertRaises(TypeError, self._dataRepo.getReferenceSetByIndex, "") referenceSetName = "id" referenceSet = references.AbstractReferenceSet(referenceSetName) self._dataRepo.addReferenceSet(referenceSet) self.assertRaises(IndexError, self._dataRepo.getReferenceSetByIndex, 1)
def testGetReference(self): path = "/references" for referenceSet in self.backend.getReferenceSets(): for reference in referenceSet.getReferences(): responseObject = self.sendGetObject(path, reference.getId(), protocol.Reference) self.verifyReferencesEqual(responseObject, reference) for badId in self.getBadIds(): referenceSet = references.AbstractReferenceSet(badId) self.verifyGetMethodFails(path, referenceSet.getId()) for badId in self.getBadIds(): self.verifyGetMethodFails(path, badId)
def testAddMultipleReferenceSet(self): firstRSLocalId = "id1" firstRS = references.AbstractReferenceSet(firstRSLocalId) secondRSLocalId = "id2" secondRS = references.AbstractReferenceSet(secondRSLocalId) self.assertEqual(self._backend.getNumReferenceSets(), 0) self.assertEqual(self._backend.getReferenceSets(), []) self._backend.addReferenceSet(firstRS) self._backend.addReferenceSet(secondRS) self.assertEqual(self._backend.getNumReferenceSets(), 2) self.assertEqual(self._backend.getReferenceSets(), [firstRS, secondRS]) self.assertEqual(self._backend.getReferenceSetByIndex(0), firstRS) self.assertEqual(self._backend.getReferenceSetByIndex(1), secondRS) self.assertEqual( self._backend.getReferenceSetByName(firstRS.getLocalId()), firstRS) self.assertEqual( self._backend.getReferenceSetByName(secondRS.getLocalId()), secondRS) self.assertEqual(self._backend.getReferenceSet(firstRS.getId()), firstRS) self.assertEqual(self._backend.getReferenceSet(secondRS.getId()), secondRS)
def getDataModelInstance(self, localId, dataPath): dataset = datasets.Dataset("ds") variantSet = variants.HtslibVariantSet(dataset, localId) variantSet.populateFromDirectory(dataPath) referenceSet = references.AbstractReferenceSet("rs") variantSet.setReferenceSet(referenceSet) if variantSet.isAnnotated(): sequenceOntology = ontologies.Ontology(paths.ontologyName) sequenceOntology.populateFromFile(paths.ontologyPath) annotationSet = variantSet.getVariantAnnotationSets()[0] annotationSet.setOntology(sequenceOntology) return annotationSet else: return variantSet
def testAddOneReferenceSet(self): referenceSetLocalId = "id" referenceSet = references.AbstractReferenceSet(referenceSetLocalId) self.assertEqual(self._backend.getNumReferenceSets(), 0) self.assertEqual(self._backend.getReferenceSets(), []) self._backend.addReferenceSet(referenceSet) self.assertEqual(self._backend.getNumReferenceSets(), 1) self.assertEqual(self._backend.getReferenceSets(), [referenceSet]) self.assertEqual(self._backend.getReferenceSetByIndex(0), referenceSet) self.assertEqual( self._backend.getReferenceSetByName(referenceSet.getLocalId()), referenceSet) self.assertEqual(self._backend.getReferenceSet(referenceSet.getId()), referenceSet)
def __init__(self, featureSetLocalName, dataPath): """ :param localId: Name of the GFF3 resource corresponding to a pair of files, .db and .gff3 :param dataPath: string representing full path to the .db file :return: """ self._dataset = datasets.Dataset(_datasetName) self._repo = datarepo.SqlDataRepository(paths.testDataRepo) self._repo.open(datarepo.MODE_READ) self._ontology = self._repo.getOntologyByName(paths.ontologyName) self._referenceSet = references.AbstractReferenceSet("test_rs") featureSetLocalName = featureSetLocalName[:-3] # remove '.db' self._testData = _testDataForFeatureSetName[featureSetLocalName] super(FeatureSetTests, self).__init__(featureSetLocalName, dataPath)
def setUp(self): self._backend = backend.Backend(datarepo.AbstractDataRepository()) self._referenceSet = references.AbstractReferenceSet(self._backend) self._reference = references.AbstractReference(self._referenceSet, "ref")
def getReferenceSet(self): return references.AbstractReferenceSet("referenceSet")
def getDataModelInstance(self, localId, dataPath): variantSet = variants.HtslibVariantSet(self._dataset, localId) variantSet.populateFromDirectory(dataPath) referenceSet = references.AbstractReferenceSet("test") variantSet.setReferenceSet(referenceSet) return variantSet
def _addReferenceSet(self, referenceSetName): self._referenceSet = references.AbstractReferenceSet(referenceSetName) self._backend.getDataRepository().addReferenceSet(self._referenceSet)
def _addReferenceSet(self, referenceSetName): self._referenceSet = references.AbstractReferenceSet(referenceSetName) self._backend.addReferenceSet(self._referenceSet)
def setUp(self): self._backend = backend.AbstractBackend() self._referenceSet = references.AbstractReferenceSet(self._backend) self._reference = references.AbstractReference(self._referenceSet, "ref")