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 setUpClass(cls):
cls.numReferences = 25
cls.backend = backend.Backend(datarepo.SimulatedDataRepository(
randomSeed=100, numDatasets=0,
numReferenceSets=1,
numReferencesPerReferenceSet=cls.numReferences))
cls.dataRepo = cls.backend.getDataRepository()
def setUpClass(cls):
cls.backend = backend.Backend(datarepo.SimulatedDataRepository(
randomSeed=100, numDatasets=3,
numVariantSets=3, numCalls=3, variantDensity=0.5,
numReferenceSets=3, numReferencesPerReferenceSet=3,
numReadGroupSets=3, numReadGroupsPerReadGroupSet=3,
numAlignments=3))
cls.dataRepo = cls.backend.getDataRepository()
def setUp(self):
self.request = protocol.SearchReadsRequest()
self.backend = backend.Backend(
datarepo.SimulatedDataRepository(numAlignments=0))
dataRepo = self.backend.getDataRepository()
referenceSet = dataRepo.getReferenceSetByIndex(0)
reference = referenceSet.getReferenceByIndex(0)
self.request.reference_id = reference.getId()
self.dataset = dataRepo.getDatasets()[0]
self.readGroupSet = self.dataset.getReadGroupSets()[0]
def otherSetup(cls):
# extract ids from a simulated data repo with the same config
repo = datarepo.SimulatedDataRepository()
dataset = repo.getDatasets()[0]
variantSet = dataset.getVariantSets()[0]
variantSetId = variantSet.getId()
cls.simulatedVariantSetId = variantSetId
requests.packages.urllib3.disable_warnings()
cls.opServer = server.OidcOpServerForTesting()
cls.opServer.start()
def configure(configFile=None, baseConfig="ProductionConfig",
port=8000, extraConfig={}):
"""
TODO Document this critical function! What does it do? What does
it assume?
"""
configStr = 'ga4gh.serverconfig:{0}'.format(baseConfig)
app.config.from_object(configStr)
if os.environ.get('GA4GH_CONFIGURATION') is not None:
app.config.from_envvar('GA4GH_CONFIGURATION')
if configFile is not None:
app.config.from_pyfile(configFile)
app.config.update(extraConfig.items())
# Setup file handle cache max size
datamodel.fileHandleCache.setMaxCacheSize(
app.config["FILE_HANDLE_CACHE_MAX_SIZE"])
# Setup CORS
cors.CORS(app, allow_headers='Content-Type')
app.serverStatus = ServerStatus()
# Allocate the backend
# We use URLs to specify the backend. Currently we have file:// URLs (or
# URLs with no scheme) for the FileSystemBackend, and special empty:// and
# simulated:// URLs for empty or simulated data sources.
dataSource = urlparse.urlparse(app.config["DATA_SOURCE"], "file")
if dataSource.scheme == "simulated":
# Ignore the query string
randomSeed = app.config["SIMULATED_BACKEND_RANDOM_SEED"]
numCalls = app.config["SIMULATED_BACKEND_NUM_CALLS"]
variantDensity = app.config["SIMULATED_BACKEND_VARIANT_DENSITY"]
numVariantSets = app.config["SIMULATED_BACKEND_NUM_VARIANT_SETS"]
numReferenceSets = app.config[
"SIMULATED_BACKEND_NUM_REFERENCE_SETS"]
numReferencesPerReferenceSet = app.config[
"SIMULATED_BACKEND_NUM_REFERENCES_PER_REFERENCE_SET"]
numAlignmentsPerReadGroup = app.config[
"SIMULATED_BACKEND_NUM_ALIGNMENTS_PER_READ_GROUP"]
dataRepository = datarepo.SimulatedDataRepository(
randomSeed=randomSeed, numCalls=numCalls,
variantDensity=variantDensity, numVariantSets=numVariantSets,
numReferenceSets=numReferenceSets,
numReferencesPerReferenceSet=numReferencesPerReferenceSet,
numAlignments=numAlignmentsPerReadGroup)
elif dataSource.scheme == "empty":
dataRepository = datarepo.EmptyDataRepository()
elif dataSource.scheme == "file":
dataRepository = datarepo.FileSystemDataRepository(os.path.join(
dataSource.netloc, dataSource.path))
dataRepository.checkConsistency()
else:
raise exceptions.ConfigurationException(
"Unsupported data source scheme: " + dataSource.scheme)
theBackend = backend.Backend(dataRepository)
theBackend.setRequestValidation(app.config["REQUEST_VALIDATION"])
theBackend.setResponseValidation(app.config["RESPONSE_VALIDATION"])
theBackend.setDefaultPageSize(app.config["DEFAULT_PAGE_SIZE"])
theBackend.setMaxResponseLength(app.config["MAX_RESPONSE_LENGTH"])
app.backend = theBackend
app.secret_key = os.urandom(SECRET_KEY_LENGTH)
app.oidcClient = None
app.tokenMap = None
app.myPort = port
if "OIDC_PROVIDER" in app.config:
# The oic client. If we're testing, we don't want to verify
# SSL certificates
app.oidcClient = oic.oic.Client(
verify_ssl=('TESTING' not in app.config))
app.tokenMap = {}
try:
app.oidcClient.provider_config(app.config['OIDC_PROVIDER'])
except requests.exceptions.ConnectionError:
configResponse = message.ProviderConfigurationResponse(
issuer=app.config['OIDC_PROVIDER'],
authorization_endpoint=app.config['OIDC_AUTHZ_ENDPOINT'],
token_endpoint=app.config['OIDC_TOKEN_ENDPOINT'],
revocation_endpoint=app.config['OIDC_TOKEN_REV_ENDPOINT'])
app.oidcClient.handle_provider_config(configResponse,
app.config['OIDC_PROVIDER'])
# The redirect URI comes from the configuration.
# If we are testing, then we allow the automatic creation of a
# redirect uri if none is configured
redirectUri = app.config.get('OIDC_REDIRECT_URI')
if redirectUri is None and 'TESTING' in app.config:
redirectUri = 'https://{0}:{1}/oauth2callback'.format(
socket.gethostname(), app.myPort)
app.oidcClient.redirect_uris = [redirectUri]
if redirectUri is []:
raise exceptions.ConfigurationException(
'OIDC configuration requires a redirect uri')
# We only support dynamic registration while testing.
if ('registration_endpoint' in app.oidcClient.provider_info and
'TESTING' in app.config):
app.oidcClient.register(
app.oidcClient.provider_info["registration_endpoint"],
redirect_uris=[redirectUri])
else:
response = message.RegistrationResponse(
client_id=app.config['OIDC_CLIENT_ID'],
client_secret=app.config['OIDC_CLIENT_SECRET'],
redirect_uris=[redirectUri],
verify_ssl=False)
app.oidcClient.store_registration_info(response)
def setUp(self):
self.request = protocol.SearchVariantsRequest()
self.backend = backend.Backend(datarepo.SimulatedDataRepository())
self.dataset = self.backend.getDataRepository().getDatasets()[0]
