def server_main(args=None):
parser = getServerParser()
parsedArgs = parser.parse_args(args)
if parsedArgs.disable_urllib_warnings:
requests.packages.urllib3.disable_warnings()
frontend.configure(parsedArgs.config_file, parsedArgs.config,
parsedArgs.port)
sslContext = None
if parsedArgs.tls or ("OIDC_PROVIDER" in frontend.app.config):
sslContext = "adhoc"
if parsedArgs.gunicorn:
options = {
'bind': '%s:%s' % (parsedArgs.host, parsedArgs.port),
'workers': int(parsedArgs.workers),
'worker_class': parsedArgs.worker_class,
'accesslog': '-', # Puts the access log on stdout
'errorlog': '-', # Puts the error log on stdout
'reload': not parsedArgs.dont_use_reloader,
}
frontend.configure(configFile=parsedArgs.config_file,
baseConfig="BaseConfig")
app = StandaloneApplication(frontend.app, options)
app.run()
else:
frontend.app.run(host=parsedArgs.host,
port=parsedArgs.port,
use_reloader=not parsedArgs.dont_use_reloader,
ssl_context=sslContext,
threaded=True)
def setUpClass(cls):
config = {
"DATA_SOURCE": paths.testDataRepo,
"DEBUG": False
}
frontend.reset()
frontend.configure(
baseConfig="DevelopmentConfig", extraConfig=config)
cls.app = frontend.app.test_client()
def setUpClass(cls):
config = {
"DATA_SOURCE": paths.testDataRepo,
"DEBUG": False
}
frontend.reset()
frontend.configure(
baseConfig="DevelopmentConfig", extraConfig=config)
cls.app = frontend.app.test_client()
def setUpClass(cls):
config = {
"DATA_SOURCE": "simulated://",
"SIMULATED_BACKEND_RANDOM_SEED": 1111,
"SIMULATED_BACKEND_NUM_CALLS": 1,
"SIMULATED_BACKEND_VARIANT_DENSITY": 1.0,
"SIMULATED_BACKEND_NUM_VARIANT_SETS": 1,
"LANDING_MESSAGE_HTML": paths.landingMessageHtml
# "DEBUG" : True
}
frontend.reset()
frontend.configure(
baseConfig="TestConfig", extraConfig=config)
cls.app = frontend.app.test_client()
# silence usually unhelpful CORS log
logging.getLogger('ga4gh.frontend.cors').setLevel(logging.CRITICAL)
# example test values
cls.backend = frontend.app.backend
cls.dataRepo = cls.backend.getDataRepository()
cls.referenceSet = cls.dataRepo.getReferenceSets()[0]
cls.referenceSetId = cls.referenceSet.getId()
cls.reference = cls.referenceSet.getReferences()[0]
cls.referenceId = cls.reference.getId()
cls.dataset = cls.backend.getDataRepository().getDatasets()[0]
cls.datasetId = cls.dataset.getId()
cls.variantSet = cls.dataset.getVariantSets()[0]
cls.variantSetId = cls.variantSet.getId()
gaVariant = cls.variantSet.getVariants("1", 0, 2**32).next()
cls.variantId = gaVariant.id
cls.callSet = cls.variantSet.getCallSets()[0]
cls.callSetId = cls.callSet.getId()
cls.readGroupSet = cls.dataset.getReadGroupSets()[0]
cls.readGroupSetId = cls.readGroupSet.getId()
cls.readGroup = cls.readGroupSet.getReadGroups()[0]
cls.readGroupId = cls.readGroup.getId()
cls.readAlignment = cls.readGroup.getReadAlignments().next()
cls.readAlignmentId = cls.readAlignment.id
cls.phenotypeAssociationSet = \
cls.dataset.getPhenotypeAssociationSets()[0]
cls.phenotypeAssociationSetId = cls.phenotypeAssociationSet.getId()
cls.association = cls.phenotypeAssociationSet.getAssociations()[0]
cls.phenotype = cls.association.phenotype
cls.phenotypeId = cls.phenotype.id
cls.featureSets = cls.dataset.getFeatureSets()
cls.genotypePhenotype = cls.phenotypeAssociationSet.getAssociations(
request=None, featureSets=cls.featureSets)[0]
cls.genotypePhenotypeId = cls.genotypePhenotype.id
cls.rnaQuantificationSet = cls.dataset.getRnaQuantificationSets()[0]
cls.rnaQuantificationSetId = cls.rnaQuantificationSet.getId()
cls.rnaQuantification = cls.rnaQuantificationSet.getRnaQuantifications(
)[0]
cls.rnaQuantificationId = cls.rnaQuantification.getId()
cls.expressionLevel = cls.rnaQuantification.getExpressionLevels(
1, 2)[0]
cls.expressionLevelId = cls.expressionLevel.getId()
def setUpClass(cls):
config = {
"DATA_SOURCE": "simulated://",
"SIMULATED_BACKEND_RANDOM_SEED": 1111,
"SIMULATED_BACKEND_NUM_CALLS": 1,
"SIMULATED_BACKEND_VARIANT_DENSITY": 1.0,
"SIMULATED_BACKEND_NUM_VARIANT_SETS": 1,
"LANDING_MESSAGE_HTML": paths.landingMessageHtml
# "DEBUG" : True
}
frontend.reset()
frontend.configure(
baseConfig="TestConfig", extraConfig=config)
cls.app = frontend.app.test_client()
# silence usually unhelpful CORS log
logging.getLogger('ga4gh.frontend.cors').setLevel(logging.CRITICAL)
# example test values
cls.backend = frontend.app.backend
cls.dataRepo = cls.backend.getDataRepository()
cls.referenceSet = cls.dataRepo.getReferenceSets()[0]
cls.referenceSetId = cls.referenceSet.getId()
cls.reference = cls.referenceSet.getReferences()[0]
cls.referenceId = cls.reference.getId()
cls.dataset = cls.backend.getDataRepository().getDatasets()[0]
cls.datasetId = cls.dataset.getId()
cls.variantSet = cls.dataset.getVariantSets()[0]
cls.variantSetId = cls.variantSet.getId()
gaVariant = cls.variantSet.getVariants("1", 0, 2**32).next()
cls.variantId = gaVariant.id
cls.callSet = cls.variantSet.getCallSets()[0]
cls.callSetId = cls.callSet.getId()
cls.readGroupSet = cls.dataset.getReadGroupSets()[0]
cls.readGroupSetId = cls.readGroupSet.getId()
cls.readGroup = cls.readGroupSet.getReadGroups()[0]
cls.readGroupId = cls.readGroup.getId()
cls.readAlignment = cls.readGroup.getReadAlignments().next()
cls.readAlignmentId = cls.readAlignment.id
cls.phenotypeAssociationSet = \
cls.dataset.getPhenotypeAssociationSets()[0]
cls.phenotypeAssociationSetId = cls.phenotypeAssociationSet.getId()
cls.association = cls.phenotypeAssociationSet.getAssociations()[0]
cls.phenotype = cls.association.phenotype
cls.phenotypeId = cls.phenotype.id
cls.featureSets = cls.dataset.getFeatureSets()
cls.genotypePhenotype = cls.phenotypeAssociationSet.getAssociations(
request=None, featureSets=cls.featureSets)[0]
cls.genotypePhenotypeId = cls.genotypePhenotype.id
cls.rnaQuantificationSet = cls.dataset.getRnaQuantificationSets()[0]
cls.rnaQuantificationSetId = cls.rnaQuantificationSet.getId()
cls.rnaQuantification = cls.rnaQuantificationSet.getRnaQuantifications(
)[0]
cls.rnaQuantificationId = cls.rnaQuantification.getId()
cls.expressionLevel = cls.rnaQuantification.getExpressionLevels(
1, 2)[0]
cls.expressionLevelId = cls.expressionLevel.getId()
def setUpClass(cls):
config = {
"DATA_SOURCE": paths.testDataRepo,
"DEBUG": False
}
logging.getLogger('ga4gh.frontend.cors').setLevel(logging.CRITICAL)
frontend.reset()
frontend.configure(
baseConfig="TestConfig", extraConfig=config)
cls.app = frontend.app.test_client()
def server_main(args=None):
parser = getServerParser()
parsedArgs = parser.parse_args(args)
if parsedArgs.disable_urllib_warnings:
requests.packages.urllib3.disable_warnings()
frontend.configure(
parsedArgs.config_file, parsedArgs.config, parsedArgs.port)
sslContext = None
if parsedArgs.tls or ("OIDC_PROVIDER" in frontend.app.config):
sslContext = "adhoc"
frontend.app.run(
host=parsedArgs.host, port=parsedArgs.port,
use_reloader=not parsedArgs.dont_use_reloader,
ssl_context=sslContext)
def server_main(args=None):
parser = getServerParser()
parsedArgs = parser.parse_args(args)
if parsedArgs.disable_urllib_warnings:
requests.packages.urllib3.disable_warnings()
frontend.configure(parsedArgs.config_file, parsedArgs.config,
parsedArgs.port)
sslContext = None
if parsedArgs.tls or ("OIDC_PROVIDER" in frontend.app.config):
sslContext = "adhoc"
frontend.app.run(host=parsedArgs.host,
port=parsedArgs.port,
use_reloader=not parsedArgs.dont_use_reloader,
ssl_context=sslContext)
def setUpClass(cls):
config = {
"DATA_SOURCE": "simulated://",
"SIMULATED_BACKEND_RANDOM_SEED": 1111,
"SIMULATED_BACKEND_NUM_CALLS": 1,
"SIMULATED_BACKEND_VARIANT_DENSITY": 1.0,
"SIMULATED_BACKEND_NUM_VARIANT_SETS": 1,
"CACHE_DIRECTORY": "/tmp/ga4gh-test"
}
frontend.reset()
frontend.configure(baseConfig="TestAuth0Config", extraConfig=config)
cls.app = frontend.app
# silence usually unhelpful CORS log
logging.getLogger('ga4gh.frontend.cors').setLevel(logging.CRITICAL)
cls.backend = frontend.app.backend
cls.client = frontend.app.test_client()
def setUpClass(cls):
config = {
"SIMULATED_BACKEND_RANDOM_SEED": 1111,
"SIMULATED_BACKEND_NUM_CALLS": 1,
"SIMULATED_BACKEND_VARIANT_DENSITY": 1.0,
"SIMULATED_BACKEND_NUM_VARIANT_SETS": 1,
"DATA_SOURCE": "simulated://",
"OIDC_CLIENT_ID": "123",
"OIDC_CLIENT_SECRET": RANDSTR,
"OIDC_PROVIDER": "http://auth.com",
"SECRET_KEY": "secret"
# "DEBUG" : True
}
frontend.reset()
frontend.configure(
baseConfig="TestOidcConfig", extraConfig=config, port=8001)
cls.app = frontend.app.test_client()
def setUpClass(cls):
config = {
"SIMULATED_BACKEND_RANDOM_SEED": 1111,
"SIMULATED_BACKEND_NUM_CALLS": 1,
"SIMULATED_BACKEND_VARIANT_DENSITY": 1.0,
"SIMULATED_BACKEND_NUM_VARIANT_SETS": 1,
"DATA_SOURCE": "simulated://",
"OIDC_CLIENT_ID": "123",
"OIDC_CLIENT_SECRET": RANDSTR,
"OIDC_PROVIDER": "https://accounts.example.com",
"SECRET_KEY": "secret"
# "DEBUG" : True
}
shutil.rmtree('/tmp/ga4gh', True)
frontend.reset()
frontend.configure(
baseConfig="TestOidcConfig", extraConfig=config, port=8001)
cls.app = frontend.app.test_client()
def setUpClass(cls):
frontend.reset()
frontend.configure(baseConfig="TestConfig")
cls.app = frontend.app.test_client()
def setUpClass(cls):
frontend.reset()
frontend.configure(baseConfig="TestConfig")
cls.app = frontend.app.test_client()
def setUpClass(cls):
frontend.reset()
frontend.configure(baseConfig="TestConfig")
frontend.app.log_exception = mock.Mock()
def setUpClass(cls):
frontend.reset()
frontend.configure(baseConfig="TestConfig")
frontend.app.log_exception = mock.Mock()
