def getDataModelInstance(self, localId, dataPath):
variantSet = variants.HtslibVariantSet(self._dataset, localId)
variantSet.populateFromDirectory(dataPath)
referenceSet = references.AbstractReferenceSet("test")
variantSet.setReferenceSet(referenceSet)
variantSet.setPatientId("patient1")
variantSet.setSampleId("sample1")
return variantSet
def __init__(self, rnaQuantificationLocalId, baseDir):
self._dataset = datasets.Dataset(_datasetName)
self._repo = datarepo.SqlDataRepository(paths.testDataRepo)
self._repo.open(datarepo.MODE_READ)
self._referenceSet = references.AbstractReferenceSet("test_rs")
rnaQuantificationId = rnaQuantificationLocalId[:-3] # remove '.db'
super(RnaQuantificationTest, self).__init__(
rnaQuantificationId, baseDir)
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 testAddMultipleReferenceSet(self):
firstRSLocalId = "id1"
firstRS = references.AbstractReferenceSet(firstRSLocalId)
secondRSLocalId = "id2"
secondRS = references.AbstractReferenceSet(secondRSLocalId)
self.assertEqual(self._dataRepo.getNumReferenceSets(), 0)
self.assertEqual(self._dataRepo.getReferenceSets(), [])
self._dataRepo.addReferenceSet(firstRS)
self._dataRepo.addReferenceSet(secondRS)
self.assertEqual(self._dataRepo.getNumReferenceSets(), 2)
self.assertEqual(self._dataRepo.getReferenceSets(),
[firstRS, secondRS])
self.assertEqual(self._dataRepo.getReferenceSetByIndex(0), firstRS)
self.assertEqual(self._dataRepo.getReferenceSetByIndex(1), secondRS)
self.assertEqual(
self._dataRepo.getReferenceSetByName(firstRS.getLocalId()),
firstRS)
self.assertEqual(
self._dataRepo.getReferenceSetByName(secondRS.getLocalId()),
secondRS)
self.assertEqual(self._dataRepo.getReferenceSet(firstRS.getId()),
firstRS)
self.assertEqual(self._dataRepo.getReferenceSet(secondRS.getId()),
secondRS)
def testAddOneReferenceSet(self):
referenceSetLocalId = "id"
referenceSet = references.AbstractReferenceSet(referenceSetLocalId)
self.assertEqual(self._dataRepo.getNumReferenceSets(), 0)
self.assertEqual(self._dataRepo.getReferenceSets(), [])
self._dataRepo.addReferenceSet(referenceSet)
self.assertEqual(self._dataRepo.getNumReferenceSets(), 1)
self.assertEqual(self._dataRepo.getReferenceSets(), [referenceSet])
self.assertEqual(self._dataRepo.getReferenceSetByIndex(0),
referenceSet)
self.assertEqual(
self._dataRepo.getReferenceSetByName(referenceSet.getLocalId()),
referenceSet)
self.assertEqual(self._dataRepo.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 getDataModelInstance(self, localId, dataPath):
dataset = datasets.Dataset("ds")
variantSet = variants.HtslibVariantSet(dataset, localId)
variantSet.populateFromDirectory(dataPath)
referenceSet = references.AbstractReferenceSet("rs")
variantSet.setReferenceSet(referenceSet)
variantSet.setPatientId("patient1")
variantSet.setSampleId("sample1")
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 setUp(self):
self._backend = backend.Backend(datarepo.AbstractDataRepository())
self._referenceSet = references.AbstractReferenceSet('refSetId')
self._reference = references.AbstractReference(self._referenceSet,
"ref")
def _addReferenceSet(self, referenceSetName):
self._referenceSet = references.AbstractReferenceSet(referenceSetName)
self._backend.getDataRepository().addReferenceSet(self._referenceSet)
def getReferenceSet(self):
return references.AbstractReferenceSet("referenceSet")