Check Junit tests. Hadoop emr6.1. Module opencga-core. Short Medium Long tests. #81
GitHub Actions / Surefire tests report hdp3.1
failed
Feb 21, 2024 in 0s
914 tests run, 129 skipped, 6 failed.
Annotations
github-actions / Surefire tests report hdp3.1
HadoopVariantStorageSearchIntersectTest.
org/eclipse/jetty/util/ssl/SslContextFactory$Client
Raw output
java.lang.NoClassDefFoundError: org/eclipse/jetty/util/ssl/SslContextFactory$Client
at org.apache.solr.client.solrj.impl.Http2SolrClient$Builder.<init>(Http2SolrClient.java:824)
at org.apache.solr.handler.component.HttpShardHandlerFactory.init(HttpShardHandlerFactory.java:316)
at org.apache.solr.handler.component.ShardHandlerFactory.newInstance(ShardHandlerFactory.java:51)
at org.apache.solr.core.CoreContainer.load(CoreContainer.java:684)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.load(EmbeddedSolrServer.java:110)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.<init>(EmbeddedSolrServer.java:106)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource$MyEmbeddedSolrServer.<init>(VariantSolrExternalResource.java:185)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:173)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:139)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.before(VariantSolrExternalResource.java:83)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:50)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:316)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:240)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:214)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:155)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.lang.ClassNotFoundException: org.eclipse.jetty.util.ssl.SslContextFactory$Client
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
... 23 more
github-actions / Surefire tests report hdp3.1
FisherTestDriverTest.testFisher
Error executing MapReduce.
Raw output
org.opencb.opencga.storage.core.exceptions.StorageEngineException: Error executing MapReduce.
at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageTest$TestMRExecutor.run(HadoopVariantStorageTest.java:539)
at org.opencb.opencga.storage.hadoop.variant.executors.MRExecutor.run(MRExecutor.java:86)
at org.opencb.opencga.storage.hadoop.variant.analysis.gwas.FisherTestDriverTest.testFisher(FisherTestDriverTest.java:97)
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.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:316)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:240)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:214)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:155)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: org.opencb.opencga.storage.core.exceptions.StorageEngineException: Error executing MapReduce. Exit code: 1
at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageTest$TestMRExecutor.run(HadoopVariantStorageTest.java:535)
... 38 more
github-actions / Surefire tests report hdp3.1
HadoopVariantExporterTest.
org/eclipse/jetty/util/ssl/SslContextFactory$Client
Raw output
java.lang.NoClassDefFoundError: org/eclipse/jetty/util/ssl/SslContextFactory$Client
at org.apache.solr.client.solrj.impl.Http2SolrClient$Builder.<init>(Http2SolrClient.java:824)
at org.apache.solr.handler.component.HttpShardHandlerFactory.init(HttpShardHandlerFactory.java:316)
at org.apache.solr.handler.component.ShardHandlerFactory.newInstance(ShardHandlerFactory.java:51)
at org.apache.solr.core.CoreContainer.load(CoreContainer.java:684)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.load(EmbeddedSolrServer.java:110)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.<init>(EmbeddedSolrServer.java:106)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource$MyEmbeddedSolrServer.<init>(VariantSolrExternalResource.java:185)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:173)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:139)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.before(VariantSolrExternalResource.java:83)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:50)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:316)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:240)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:214)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:155)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.lang.ClassNotFoundException: org.eclipse.jetty.util.ssl.SslContextFactory$Client
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
... 23 more
github-actions / Surefire tests report hdp3.1
HadoopVariantSearchIndexTest.testSearchIndexRemoveSearchIndex
org/eclipse/jetty/util/ssl/SslContextFactory$Client
Raw output
java.lang.NoClassDefFoundError: org/eclipse/jetty/util/ssl/SslContextFactory$Client
at org.apache.solr.client.solrj.impl.Http2SolrClient$Builder.<init>(Http2SolrClient.java:824)
at org.apache.solr.handler.component.HttpShardHandlerFactory.init(HttpShardHandlerFactory.java:316)
at org.apache.solr.handler.component.ShardHandlerFactory.newInstance(ShardHandlerFactory.java:51)
at org.apache.solr.core.CoreContainer.load(CoreContainer.java:684)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.load(EmbeddedSolrServer.java:110)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.<init>(EmbeddedSolrServer.java:106)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource$MyEmbeddedSolrServer.<init>(VariantSolrExternalResource.java:185)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:173)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:139)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.before(VariantSolrExternalResource.java:83)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:50)
at org.junit.rules.ExpectedException$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.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:316)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:240)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:214)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:155)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.lang.ClassNotFoundException: org.eclipse.jetty.util.ssl.SslContextFactory$Client
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
... 36 more
github-actions / Surefire tests report hdp3.1
HadoopVariantSearchIndexTest.testIncrementalIndex
org/eclipse/jetty/util/ssl/SslContextFactory$Client
Raw output
java.lang.NoClassDefFoundError: org/eclipse/jetty/util/ssl/SslContextFactory$Client
at org.apache.solr.client.solrj.impl.Http2SolrClient$Builder.<init>(Http2SolrClient.java:824)
at org.apache.solr.handler.component.HttpShardHandlerFactory.init(HttpShardHandlerFactory.java:316)
at org.apache.solr.handler.component.ShardHandlerFactory.newInstance(ShardHandlerFactory.java:51)
at org.apache.solr.core.CoreContainer.load(CoreContainer.java:684)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.load(EmbeddedSolrServer.java:110)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.<init>(EmbeddedSolrServer.java:106)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource$MyEmbeddedSolrServer.<init>(VariantSolrExternalResource.java:185)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:173)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:139)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.before(VariantSolrExternalResource.java:83)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:50)
at org.junit.rules.ExpectedException$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.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:316)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:240)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:214)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:155)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.lang.ClassNotFoundException: org.eclipse.jetty.util.ssl.SslContextFactory$Client
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
... 36 more
github-actions / Surefire tests report hdp3.1
HadoopVariantSearchIndexTest.testSearchIndexAfterRemove
org/eclipse/jetty/util/ssl/SslContextFactory$Client
Raw output
java.lang.NoClassDefFoundError: org/eclipse/jetty/util/ssl/SslContextFactory$Client
at org.apache.solr.client.solrj.impl.Http2SolrClient$Builder.<init>(Http2SolrClient.java:824)
at org.apache.solr.handler.component.HttpShardHandlerFactory.init(HttpShardHandlerFactory.java:316)
at org.apache.solr.handler.component.ShardHandlerFactory.newInstance(ShardHandlerFactory.java:51)
at org.apache.solr.core.CoreContainer.load(CoreContainer.java:684)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.load(EmbeddedSolrServer.java:110)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.<init>(EmbeddedSolrServer.java:106)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource$MyEmbeddedSolrServer.<init>(VariantSolrExternalResource.java:185)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:173)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.create(VariantSolrExternalResource.java:139)
at org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource.before(VariantSolrExternalResource.java:83)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:50)
at org.junit.rules.ExpectedException$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.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:316)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:240)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:214)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:155)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.lang.ClassNotFoundException: org.eclipse.jetty.util.ssl.SslContextFactory$Client
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
... 36 more
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