def setUp(): """ Set up the test Flask app. """ global _app frontend.configure(baseConfig="TestConfig") _app = frontend.app.test_client()
def setUpClass(cls): # silence usually unhelpful CORS log logging.getLogger('ga4gh.frontend.cors').setLevel(logging.CRITICAL) cls.numReferenceSets = 5 cls.numReferencesPerReferenceSet = 3 cls.numAlignmentsPerReadGroup = 2 config = { "DATA_SOURCE": "__SIMULATED__", "SIMULATED_BACKEND_RANDOM_SEED": 1111, "SIMULATED_BACKEND_NUM_CALLS": 0, "SIMULATED_BACKEND_VARIANT_DENSITY": 1.0, "SIMULATED_BACKEND_NUM_VARIANT_SETS": 10, "SIMULATED_BACKEND_NUM_REFERENCE_SETS": cls.numReferenceSets, "SIMULATED_BACKEND_NUM_REFERENCES_PER_REFERENCE_SET": cls.numReferencesPerReferenceSet, "SIMULATED_BACKEND_NUM_ALIGNMENTS_PER_READ_GROUP": cls.numAlignmentsPerReadGroup, } 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, # "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.referenceSet = cls.backend.getReferenceSets()[0] cls.referenceSetId = cls.referenceSet.getId() cls.reference = cls.referenceSet.getReferences()[0] cls.referenceId = cls.reference.getId() cls.dataset = cls.backend.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
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 server_main(parser=None): if parser is None: parser = argparse.ArgumentParser( description="GA4GH reference server") addGlobalOptions(parser) args = parser.parse_args() frontend.configure(args.config_file, args.config) frontend.app.run( host="0.0.0.0", port=args.port, use_reloader=not args.dont_use_reloader)
def setUpClass(cls): config = { "DATA_SOURCE": "__SIMULATED__", "SIMULATED_BACKEND_RANDOM_SEED": 1111, "SIMULATED_BACKEND_NUM_CALLS": 0, "SIMULATED_BACKEND_VARIANT_DENSITY": 1.0, "SIMULATED_BACKEND_NUM_VARIANT_SETS": 10, } frontend.configure(baseConfig="TestConfig", extraConfig=config) cls.app = frontend.app.test_client()
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, "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 setUp(self): config = { "DATA_SOURCE": "__SIMULATED__", "SIMULATED_BACKEND_RANDOM_SEED": 1111, "SIMULATED_BACKEND_NUM_CALLS": 0, "SIMULATED_BACKEND_VARIANT_DENSITY": 1.0, "SIMULATED_BACKEND_NUM_VARIANT_SETS": 10, } frontend.configure( baseConfig="TestConfig", extraConfig=config) global _app _app = frontend.app.test_client()
def server_main(parser=None): if parser is None: parser = argparse.ArgumentParser( description="GA4GH reference server") addGlobalOptions(parser) args = parser.parse_args() frontend.configure(args.config_file, args.config, args.port) sslContext = None if args.tls or ("OIDC_PROVIDER" in frontend.app.config): sslContext = "adhoc" frontend.app.run( host="0.0.0.0", port=args.port, use_reloader=not args.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 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, # "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)
def server_main(parser=None): if parser is None: parser = argparse.ArgumentParser(description="GA4GH reference server") # Add global options parser.add_argument("--port", "-P", default=8000, type=int, help="The port to listen on") parser.add_argument("--config", "-C", default='DefaultConfig', type=str, help="The configuration to use") parser.add_argument("--config-file", "-F", type=str, help="The configuration file to use") subparsers = parser.add_subparsers(title='subcommands', ) # help helpParser = subparsers.add_parser("help", description="ga4gh_server help", help="show this help message and exit") # Wormtable backend wtbParser = subparsers.add_parser( "wormtable", description="Serve the API using a wormtable based backend.", help="Serve data from tables.") wtbParser.add_argument( "dataDir", help="The directory containing the wormtables to be served.") wtbParser.set_defaults(variantSetClass=variants.WormtableVariantSet) # Tabix tabixParser = subparsers.add_parser( "tabix", description="Serve the API using a tabix based backend.", help="Serve data from Tabix indexed VCFs") tabixParser.add_argument("dataDir", help="The directory containing VCFs") tabixParser.set_defaults(variantSetClass=variants.TabixVariantSet) args = parser.parse_args() if "variantSetClass" not in args: parser.print_help() else: frontend.configure(args.config, args.config_file) frontend.app.backend = backend.Backend(args.dataDir, args.variantSetClass) frontend.app.run(host="0.0.0.0", port=args.port, debug=True)
def server_main(parser=None): if parser is None: parser = argparse.ArgumentParser( description="GA4GH reference server") # Add global options parser.add_argument( "--port", "-P", default=8000, type=int, help="The port to listen on") parser.add_argument( "--config", "-C", default='DefaultConfig', type=str, help="The configuration to use") parser.add_argument( "--config-file", "-F", type=str, help="The configuration file to use") subparsers = parser.add_subparsers(title='subcommands',) # help subparsers.add_parser( "help", description="ga4gh_server help", help="show this help message and exit") # Wormtable backend wtbParser = subparsers.add_parser( "wormtable", description="Serve the API using a wormtable based backend.", help="Serve data from tables.") wtbParser.add_argument( "dataDir", help="The directory containing the wormtables to be served.") wtbParser.set_defaults(variantSetClass=variants.WormtableVariantSet) # Tabix tabixParser = subparsers.add_parser( "tabix", description="Serve the API using a tabix based backend.", help="Serve data from Tabix indexed VCFs") tabixParser.add_argument( "dataDir", help="The directory containing VCFs") tabixParser.set_defaults(variantSetClass=variants.TabixVariantSet) args = parser.parse_args() if "variantSetClass" not in args: parser.print_help() else: frontend.configure(args.config, args.config_file) frontend.app.backend = backend.Backend( args.dataDir, args.variantSetClass) frontend.app.run(host="0.0.0.0", port=args.port, debug=True)
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, "OIDC_CLIENT_ID": "123", "OIDC_CLIENT_SECRET": RANDSTR, "OIDC_PROVIDER": "http://auth.com" # "DEBUG" : True } frontend.reset() frontend.configure(baseConfig="TestOidcConfig", extraConfig=config, port=8001) cls.app = frontend.app.test_client()
def server_main(parser=None): if parser is None: parser = argparse.ArgumentParser(description="GA4GH reference server") addServerOptions(parser) args = parser.parse_args() if args.disable_urllib_warnings: requests.packages.urllib3.disable_warnings() frontend.configure(args.config_file, args.config, args.port) sslContext = None if args.tls or ("OIDC_PROVIDER" in frontend.app.config): sslContext = "adhoc" frontend.app.run(host=args.host, port=args.port, use_reloader=not args.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, "OIDC_CLIENT_ID": "123", "OIDC_CLIENT_SECRET": RANDSTR, "OIDC_PROVIDER": "http://auth.com" # "DEBUG" : True } frontend.reset() frontend.configure( baseConfig="TestOidcConfig", extraConfig=config, port=8001) cls.app = frontend.app.test_client()
def server_main(parser=None): if parser is None: parser = argparse.ArgumentParser( description="GA4GH reference server") addServerOptions(parser) args = parser.parse_args() if args.disable_urllib_warnings: requests.packages.urllib3.disable_warnings() frontend.configure( args.config_file, args.config, args.port) sslContext = None if args.tls or ("OIDC_PROVIDER" in frontend.app.config): sslContext = "adhoc" frontend.app.run( host=args.host, port=args.port, use_reloader=not args.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, # "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
def setUpClass(cls): # silence usually unhelpful CORS log logging.getLogger("ga4gh.frontend.cors").setLevel(logging.CRITICAL) # Set the random seed to make tests reproducible. random.seed(1) config = { "DATA_SOURCE": "__SIMULATED__", "SIMULATED_BACKEND_RANDOM_SEED": 1111, "SIMULATED_BACKEND_NUM_CALLS": 5, "SIMULATED_BACKEND_VARIANT_DENSITY": 1.0, "SIMULATED_BACKEND_NUM_VARIANT_SETS": 4, "SIMULATED_BACKEND_NUM_REFERENCE_SETS": 3, "SIMULATED_BACKEND_NUM_REFERENCES_PER_REFERENCE_SET": 4, "SIMULATED_BACKEND_NUM_ALIGNMENTS_PER_READ_GROUP": 5, } frontend.reset() frontend.configure(baseConfig="TestConfig", extraConfig=config) cls.app = frontend.app.test_client()
def setUpClass(cls): # silence usually unhelpful CORS log logging.getLogger('ga4gh.frontend.cors').setLevel(logging.CRITICAL) # Set the random seed to make tests reproducible. random.seed(1) config = { "DATA_SOURCE": "simulated://", "SIMULATED_BACKEND_RANDOM_SEED": 1111, "SIMULATED_BACKEND_NUM_CALLS": 5, "SIMULATED_BACKEND_VARIANT_DENSITY": 1.0, "SIMULATED_BACKEND_NUM_VARIANT_SETS": 4, "SIMULATED_BACKEND_NUM_REFERENCE_SETS": 3, "SIMULATED_BACKEND_NUM_REFERENCES_PER_REFERENCE_SET": 4, "SIMULATED_BACKEND_NUM_ALIGNMENTS_PER_READ_GROUP": 5 } 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, # "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
def setUp(self): frontend.configure("TestConfig") frontend.app.backend = backend.MockBackend() self.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") cls.app = frontend.app.test_client()
def setUpClass(cls): frontend.reset() frontend.configure(baseConfig="TestConfig")
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): reload(frontend) frontend.configure(baseConfig="TestConfig") cls.app = frontend.app.test_client()