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 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 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")
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()
def setUpClass(cls):
frontend.reset()
frontend.configure(baseConfig="TestConfig")