def __init__(self, args):
self._key = args.key
# TODO this is an experimental addition which is useful for
# testing. We should think about this and document it if we
# this it's a useful feature. There is an argument for pushing
# the backend instantiation into the client, and letting the
# client be a factory, instantiating the correct Client class
# depending on the prefix.
filePrefix = "file://"
if args.baseUrl.startswith(filePrefix):
dataDir = args.baseUrl[len(filePrefix):]
theBackend = backend.FileSystemBackend(dataDir)
self._client = client.LocalClient(theBackend)
else:
self._client = client.HttpClient(args.baseUrl,
verbosityToLogLevel(args.verbose),
self._key)
def setUp(self):
self._dataDir = os.path.join("tests", "data")
self._variantsDir = os.path.join(self._dataDir, "variants")
self._vcfs = {}
self._variants = []
self._referenceNames = set()
self._chromFileMap = {}
for relativePath in os.listdir(self._variantsDir):
pathToFiles = os.path.join(self._variantsDir, relativePath)
self._vcfs[relativePath] = []
for vcfFile in glob.glob(os.path.join(pathToFiles, "*.vcf.gz")):
self._chromFileMap[relativePath] = {}
self._vcfs[relativePath].append(vcfFile)
vcf = pysam.VariantFile(filename=vcfFile)
for chrom in vcf.index:
self._chromFileMap[relativePath][chrom] = vcf
self._backend = backend.FileSystemBackend(self._dataDir)
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.FileSystemBackend("tests/data")
self._client = client.LocalClient(self._backend)
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._dataDir = "tests/data"
self._dataUrl = "file://{}".format(self._dataDir)
self._backend = backend.FileSystemBackend(self._dataDir)
self._client = client.LocalClient(self._backend)
def setUp(self):
self._dataDir = os.path.join("tests", "data")
self._backend = backend.FileSystemBackend(self._dataDir)