Merge pull request #2391 from opencb/TASK-5609 #843
GitHub Actions / Surefire tests report
failed
Feb 8, 2024 in 0s
1535 tests run, 91 skipped, 2 failed.
Annotations
github-actions / Surefire tests report
ExomiserInterpretationAnalysisTest.
Error annotating.
Raw output
org.opencb.opencga.storage.core.exceptions.StoragePipelineException: Error annotating.
at org.opencb.opencga.storage.core.variant.VariantStorageEngine.annotateLoadedFiles(VariantStorageEngine.java:408)
at org.opencb.opencga.storage.core.variant.VariantStorageEngine.index(VariantStorageEngine.java:309)
at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine.index(HadoopVariantStorageEngine.java:177)
at org.opencb.opencga.analysis.variant.manager.operations.VariantFileIndexerOperationManager.indexFiles(VariantFileIndexerOperationManager.java:303)
at org.opencb.opencga.analysis.variant.manager.operations.VariantFileIndexerOperationManager.index(VariantFileIndexerOperationManager.java:125)
at org.opencb.opencga.analysis.variant.manager.VariantStorageManager.lambda$index$2(VariantStorageManager.java:204)
at org.opencb.opencga.analysis.variant.manager.VariantStorageManager.secureTool(VariantStorageManager.java:1233)
at org.opencb.opencga.analysis.variant.manager.VariantStorageManager.secureOperation(VariantStorageManager.java:1182)
at org.opencb.opencga.analysis.variant.manager.VariantStorageManager.index(VariantStorageManager.java:202)
at org.opencb.opencga.analysis.variant.manager.VariantStorageManager.index(VariantStorageManager.java:197)
at org.opencb.opencga.analysis.clinical.ClinicalAnalysisUtilsTest.getClinicalTest(ClinicalAnalysisUtilsTest.java:77)
at org.opencb.opencga.analysis.clinical.exomiser.ExomiserInterpretationAnalysisTest.setUp(ExomiserInterpretationAnalysisTest.java:50)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.junit.runners.Suite.runChild(Suite.java:128)
at org.junit.runners.Suite.runChild(Suite.java:27)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.lang.IllegalArgumentException: Unable to access cellbase url 'https://ws.zettagenomics.com/cellbase', version 'v5.1'
at org.opencb.opencga.core.cellbase.CellBaseValidator.validate(CellBaseValidator.java:153)
at org.opencb.opencga.core.cellbase.CellBaseValidator.validate(CellBaseValidator.java:143)
at org.opencb.opencga.storage.core.variant.annotation.annotators.CellBaseRestVariantAnnotator.<init>(CellBaseRestVariantAnnotator.java:75)
at org.opencb.opencga.storage.core.variant.annotation.annotators.VariantAnnotatorFactory.buildVariantAnnotator(VariantAnnotatorFactory.java:75)
at org.opencb.opencga.storage.core.variant.VariantStorageEngine.newVariantAnnotationManager(VariantStorageEngine.java:463)
at org.opencb.opencga.storage.core.variant.VariantStorageEngine.annotate(VariantStorageEngine.java:348)
at org.opencb.opencga.storage.core.variant.VariantStorageEngine.annotateLoadedFiles(VariantStorageEngine.java:406)
... 43 more
Caused by: javax.ws.rs.ServiceUnavailableException: HTTP 503 Service Temporarily Unavailable
at org.glassfish.jersey.client.JerseyInvocation.convertToException(JerseyInvocation.java:957)
at org.glassfish.jersey.client.JerseyInvocation.translate(JerseyInvocation.java:739)
at org.glassfish.jersey.client.JerseyInvocation.lambda$invoke$1(JerseyInvocation.java:623)
at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
at org.glassfish.jersey.internal.Errors.process(Errors.java:205)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:390)
at org.glassfish.jersey.client.JerseyInvocation.invoke(JerseyInvocation.java:621)
at org.glassfish.jersey.client.JerseyInvocation$Builder.method(JerseyInvocation.java:404)
at org.glassfish.jersey.client.JerseyInvocation$Builder.get(JerseyInvocation.java:300)
at org.opencb.cellbase.client.rest.ParentRestClient.restCall(ParentRestClient.java:483)
at org.opencb.cellbase.client.rest.ParentRestClient.robustRestCall(ParentRestClient.java:377)
at org.opencb.cellbase.client.rest.ParentRestClient.fetchData(ParentRestClient.java:308)
at org.opencb.cellbase.client.rest.ParentRestClient.execute(ParentRestClient.java:242)
at org.opencb.cellbase.client.rest.ParentRestClient.execute(ParentRestClient.java:223)
at org.opencb.cellbase.client.rest.ParentRestClient.execute(ParentRestClient.java:213)
at org.opencb.cellbase.client.rest.ParentRestClient.execute(ParentRestClient.java:205)
at org.opencb.cellbase.client.rest.MetaClient.species(MetaClient.java:55)
at org.opencb.cellbase.client.rest.MetaClient.species(MetaClient.java:51)
at org.opencb.opencga.core.cellbase.CellBaseValidator.validate(CellBaseValidator.java:151)
... 49 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.loadClinicalAnalysesTest
expected:<1> but was:<3>
Raw output
java.lang.AssertionError: expected:<1> but was:<3>
at org.junit.Assert.fail(Assert.java:89)
at org.junit.Assert.failNotEquals(Assert.java:835)
at org.junit.Assert.assertEquals(Assert.java:647)
at org.junit.Assert.assertEquals(Assert.java:633)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.loadClinicalAnalysesTest(ClinicalAnalysisManagerTest.java:3698)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.junit.runners.Suite.runChild(Suite.java:128)
at org.junit.runners.Suite.runChild(Suite.java:27)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
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