Python reset Beispiele

Beispiel #1

    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()

Beispiel #2

Datei: test_views.py Projekt: diekhans/ga4gh-server

    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

Beispiel #3

Datei: test_g2p.py Projekt: david4096/server-1

 def setUpClass(cls):
     config = {
         "DATA_SOURCE": paths.testDataRepo,
         "DEBUG": False
     }
     frontend.reset()
     frontend.configure(
         baseConfig="DevelopmentConfig", extraConfig=config)
     cls.app = frontend.app.test_client()

Beispiel #4

Datei: test_views.py Projekt: david4096/server-1

    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()

Beispiel #5

 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()

Beispiel #6

Datei: test_views.py Projekt: ga4ghpoc/server

    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()

Beispiel #7

Datei: test_views.py Projekt: UMMS-Biocore/ga4gh-server

 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)

Beispiel #8

Datei: test_oidc.py Projekt: malisas/server

 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()

Beispiel #9

Datei: test_oidc.py Projekt: UMMS-Biocore/ga4gh-server

 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()

Beispiel #10

 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()

Beispiel #11

Datei: test_simulated_stack.py Projekt: malisas/server

 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()

Beispiel #12

Datei: test_g2p.py Projekt: malisas/server

    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

Beispiel #13

Datei: test_views.py Projekt: bosz/server

    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

Beispiel #14

 def setUpClass(cls):
     config = {"DATA_SOURCE": paths.testDataRepo, "DEBUG": False}
     frontend.reset()
     frontend.configure(baseConfig="DevelopmentConfig", extraConfig=config)
     cls.app = frontend.app.test_client()

Beispiel #15

 def setUpClass(cls):
     frontend.reset()
     frontend.configure(baseConfig="TestConfig")
     frontend.app.log_exception = mock.Mock()

Beispiel #16

Datei: test_exceptions.py Projekt: ljishen/server

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

Beispiel #17

Datei: test_protocol_errors.py Projekt: ljishen/server

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

Beispiel #18

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

Beispiel #19

Datei: test_protocol_errors.py Projekt: Arc39/server

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