def setUpClass(cls):
cls.numReferences = 25
cls.backend = backend.SimulatedBackend(
randomSeed=100,
numDatasets=0,
numReferenceSets=1,
numReferencesPerReferenceSet=cls.numReferences)
def setUpClass(cls):
cls.backend = backend.SimulatedBackend(
randomSeed=100, numDatasets=3,
numVariantSets=3, numCalls=3, variantDensity=0.5,
numReferenceSets=3, numReferencesPerReferenceSet=3,
numReadGroupSets=3, numReadGroupsPerReadGroupSet=3,
numAlignments=3)
def setUp(self):
self.request = protocol.SearchReadsRequest()
self.backend = backend.SimulatedBackend(numAlignments=0)
referenceSet = self.backend.getReferenceSetByIndex(0)
reference = referenceSet.getReferenceByIndex(0)
self.request.referenceId = reference.getId()
self.dataset = self.backend.getDatasets()[0]
self.readGroupSet = self.dataset.getReadGroupSets()[0]
def setUp(self):
self.request = protocol.SearchReadsRequest()
self.request.referenceId = "chr1"
self.backend = backend.SimulatedBackend()
self.datasetId = self.backend.getDatasetIds()[0]
self.dataset = self.backend.getDataset(self.datasetId)
self.readGroupSetLocalId = "aReadGroupSet"
self.readGroupLocalId = "aReadGroup"
self.readGroupSet = reads.AbstractReadGroupSet(
self.dataset, self.readGroupSetLocalId)
def configure(configFile=None, baseConfig="ProductionConfig", 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 CORS
cors.CORS(app, allow_headers='Content-Type')
app.serverStatus = ServerStatus()
# Allocate the backend
# TODO is this a good way to determine what type of backend we should
# instantiate? We should think carefully about this. The approach of
# using the special strings __SIMULATED__ and __EMPTY__ seems OK for
# now, but is certainly not ideal.
dataSource = app.config["DATA_SOURCE"]
if dataSource == "__SIMULATED__":
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"]
theBackend = backend.SimulatedBackend(randomSeed, numCalls,
variantDensity, numVariantSets)
elif dataSource == "__EMPTY__":
theBackend = backend.EmptyBackend()
else:
theBackend = backend.FileSystemBackend(dataSource)
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
def setUp(self):
self._backend = backend.SimulatedBackend(numCalls=100,
numVariantSets=10)
def setUp(self):
self.request = protocol.SearchVariantsRequest()
self.backend = backend.SimulatedBackend()
self.dataset = self.backend.getDatasets()[0]
def setUp(self):
self.request = protocol.SearchVariantsRequest()
self.backend = backend.SimulatedBackend()
self.datasetId = self.backend.getDatasetIds()[0]
self.dataset = self.backend.getDataset(self.datasetId)
self.variantSetLocalId = 'variantSet'
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
# TODO is this a good way to determine what type of backend we should
# instantiate? We should think carefully about this. The approach of
# using the special strings __SIMULATED__ and __EMPTY__ seems OK for
# now, but is certainly not ideal.
dataSource = app.config["DATA_SOURCE"]
if dataSource == "__SIMULATED__":
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"]
numAlignments = app.config[
"SIMULATED_BACKEND_NUM_ALIGNMENTS_PER_READ_GROUP"]
theBackend = backend.SimulatedBackend(randomSeed, numCalls,
variantDensity, numVariantSets,
numReferenceSets,
numReferencesPerReferenceSet,
numAlignments)
elif dataSource == "__EMPTY__":
theBackend = backend.EmptyBackend()
else:
theBackend = backend.FileSystemBackend(dataSource)
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.SimulatedBackend()
self.datasetId = self.backend.getDatasetIds()[0]
self.variantSetId = "{}:variantSetId".format(self.datasetId)
def setUp(self):
self.request = protocol.SearchReadsRequest()
self.backend = backend.SimulatedBackend()
self.datasetId = self.backend.getDatasetIds()[0]
self.readGroupId = "{}:readGroupId".format(self.datasetId)
