def testMultipleOidcClients(self):
serverUrl = self.server.getUrl()
key = getClientKey(serverUrl, 'diana', 'krall')
key2 = getClientKey(serverUrl, 'upper', 'crust')
client1 = client.ClientForTesting(serverUrl,
flags="--key {}".format(key))
client2 = client.ClientForTesting(serverUrl,
flags="--key {}".format(key2))
self.runVariantsRequest(client1)
self.runVariantsRequest(client2)
client1.cleanup()
client2.cleanup()
def testEndToEnd(self):
# extract ids from a simulated data repo with the same config
repo = datarepo.SimulatedDataRepository()
dataset = repo.getDatasets()[0]
datasetId = dataset.getId()
variantSet = dataset.getVariantSets()[0]
variantSetId = variantSet.getId()
readGroupSet = dataset.getReadGroupSets()[0]
readGroupId = readGroupSet.getReadGroups()[0].getId()
referenceSet = repo.getReferenceSets()[0]
referenceSetId = referenceSet.getId()
referenceId = referenceSet.getReferences()[0].getId()
variantAnnotationSetId = \
variantSet.getVariantAnnotationSets()[0].getId()
self.simulatedDatasetId = datasetId
self.simulatedVariantSetId = variantSetId
self.simulatedReadGroupId = readGroupId
self.simulatedReferenceSetId = referenceSetId
self.simulatedReferenceId = referenceId
self.simulatedVariantAnnotationSetId = variantAnnotationSetId
self.client = client.ClientForTesting(self.server.getUrl())
self.runVariantsRequest()
self.assertLogsWritten()
self.runReadsRequest()
self.runReferencesRequest()
self.runVariantSetsRequestDatasetTwo()
self.runVariantAnnotationsRequest()
self.runGetVariantAnnotationSetsRequest()
self.client.cleanup()
def testOidc(self):
serverUrl = self.server.getUrl()
key = getClientKey(serverUrl, 'diana', 'krall')
test_client = client.ClientForTesting(serverUrl,
flags="--key {}".format(key))
self.runVariantsRequest(test_client)
test_client.cleanup()
def testOidcBadLoginKey(self):
serverUrl = self.server.getUrl()
test_client = client.ClientForTesting(serverUrl,
flags="--key {}".format('ABC'))
self.assertRaises(subprocess.CalledProcessError,
self.runVariantSetRequest, test_client)
test_client.cleanup()
def testEndToEnd(self):
self.client = client.ClientForTesting(self.server.getUrl())
self.runVariantsRequest()
self.assertLogsWritten()
self.runReadsRequest()
self.runReferencesRequest()
self.runVariantSetsRequestDatasetTwo()
self.client.cleanup()
def testOidcBadLoginKey(self):
serverUrl = self.server.getUrl()
test_client = client.ClientForTesting(serverUrl,
flags="--key {}".format('ABC'))
with self.assertRaises(subprocess.CalledProcessError):
test_client.runCommand(
"variants-search -s 0 -e 2 -V simulatedDataset1:simVs0",
debugOnFail=False)
test_client.cleanup()
def testBamFetch(self):
self.client = client.ClientForTesting(self.server.getUrl())
self.readGroupIds = ('dataset1:remoteTest:'
'wgEncodeUwRepliSeqBg02esG1bAlnRep1_sample')
self.runClientCmd(
self.client, "reads-search --readGroupIds '{}' "
"--referenceId chr1 ".format(self.readGroupIds))
self._assertLogsWritten()
self.client.cleanup()
def testEndToEnd(self):
self.simulatedDatasetId = "c2ltdWxhdGVkRGF0YXNldDA="
self.simulatedVariantSetId = "c2ltdWxhdGVkRGF0YXNldDA6c2ltVnMw"
self.simulatedReadGroupId = "c2ltdWxhdGVkRGF0YXNldDA6c2ltUmdzMDpyZzA="
self.simulatedReferenceSetId = "cmVmZXJlbmNlU2V0MA=="
self.simulatedReferenceId = "cmVmZXJlbmNlU2V0MDpzcnMw"
self.client = client.ClientForTesting(self.server.getUrl())
self.runVariantsRequest()
self.assertLogsWritten()
self.runReadsRequest()
self.runReferencesRequest()
self.runVariantSetsRequestDatasetTwo()
self.client.cleanup()
def testEndToEnd(self):
self.simulatedDatasetId = datamodel.DatasetCompoundId.obfuscate(
paths.simulatedDatasetId)
self.simulatedVariantSetId = \
datamodel.VariantSetCompoundId.obfuscate(
paths.simulatedVariantSetId)
self.simulatedReadGroupId = datamodel.ReadGroupCompoundId.obfuscate(
paths.simulatedReadGroupId)
self.simulatedReferenceSetId = \
datamodel.ReferenceSetCompoundId.obfuscate(
paths.simulatedReferenceSetId)
self.simulatedReferenceId = \
datamodel.ReferenceCompoundId.obfuscate(
paths.simulatedReferenceId)
self.simulatedVariantAnnotationSetId = \
datamodel.VariantAnnotationSetCompoundId.obfuscate(
paths.simulatedVariantAnnotationSetId)
self.client = client.ClientForTesting(self.server.getUrl())
self.runVariantsRequest()
self.assertLogsWritten()
self.runReadsRequest()
self.runReferencesRequest()
self.runVariantSetsRequestDatasetTwo()
self.client.cleanup()
def testVcfFetch(self):
self.client = client.ClientForTesting(self.server.getUrl())
self.runClientCmd(self.client,
"variants-search -V dataset1:remoteTest")
self._assertLogsWritten()
self.client.cleanup()
