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": 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 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 tearDownClass(cls): shutil.rmtree('/tmp/ga4gh-test', True) frontend.reset()
def setUpClass(cls): frontend.reset() frontend.configure(baseConfig="TestConfig") frontend.app.log_exception = mock.Mock()