Prepare next release 2.12.6.1-SNAPSHOT #982
1418 tests run, 48 skipped, 81 failed.
Annotations
github-actions / Surefire tests report
ClinicalInterpretationAnalysisTest.
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUpCatalogManager(AbstractClinicalManagerTest.java:103)
at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUp(AbstractClinicalManagerTest.java:86)
at org.opencb.opencga.analysis.clinical.ClinicalAnalysisUtilsTest.getClinicalTest(ClinicalAnalysisUtilsTest.java:52)
at org.opencb.opencga.analysis.clinical.ClinicalInterpretationAnalysisTest.setUp(ClinicalInterpretationAnalysisTest.java:79)
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.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e501bf75-0190-0007-0001-440b83ac0886-6040662653773
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 46 more
github-actions / Surefire tests report
ExomiserInterpretationAnalysisTest.
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUpCatalogManager(AbstractClinicalManagerTest.java:103)
at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUp(AbstractClinicalManagerTest.java:86)
at org.opencb.opencga.analysis.clinical.ClinicalAnalysisUtilsTest.getClinicalTest(ClinicalAnalysisUtilsTest.java:52)
at org.opencb.opencga.analysis.clinical.exomiser.ExomiserInterpretationAnalysisTest.setUp(ExomiserInterpretationAnalysisTest.java:58)
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.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e50230d0-0190-0007-0001-7c34fb6de658-6069703802379
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 46 more
github-actions / Surefire tests report
VariantCatalogQueryUtilsTest.
Error computing pedigree graph for family f1
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.analysis.variant.manager.VariantCatalogQueryUtilsTest.setUp(VariantCatalogQueryUtilsTest.java:138)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e501266c-0190-0007-0001-7e133bf9a9fb-6001377335357
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 41 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithEmptyInterpretations
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithEmptyInterpretations(ClinicalAnalysisManagerTest.java:2666)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c070db-0190-0007-0001-1478ec588a7b-1760879089157
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.createClinicalAnalysisWithPanels
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createClinicalAnalysisWithPanels(ClinicalAnalysisManagerTest.java:2864)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c0856b-0190-0007-0001-a92dd3ea8c00-1766002872843
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 55 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.searchClinicalAnalysisByProband
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchClinicalAnalysisByProband(ClinicalAnalysisManagerTest.java:2598)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c0924e-0190-0007-0001-49153e09da07-1769274907957
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.updatePrimarySecondaryLockedInterpretationTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updatePrimarySecondaryLockedInterpretationTest(ClinicalAnalysisManagerTest.java:2390)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c09f23-0190-0007-0001-766f9d876a42-1772599128150
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.updateCustomConsentTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateCustomConsentTest(ClinicalAnalysisManagerTest.java:1764)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c0c4cb-0190-0007-0001-b853c7c5b6b2-1782159717687
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.createAndTestStatusIdIsNotNull
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createAndTestStatusIdIsNotNull(ClinicalAnalysisManagerTest.java:230)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c0d111-0190-0007-0001-4337f9530b04-1785299811820
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 55 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.updateInterpretationFindingsTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateInterpretationFindingsTest(ClinicalAnalysisManagerTest.java:1949)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c0ea99-0190-0007-0001-4b7be0d85629-1791843793519
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.deleteLockedClinicalAnalysis
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteLockedClinicalAnalysis(ClinicalAnalysisManagerTest.java:2761)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c0f710-0190-0007-0001-85e4047d8731-1795017594417
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.searchInterpretationVersion
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchInterpretationVersion(ClinicalAnalysisManagerTest.java:2067)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c1032b-0190-0007-0001-dd94b002b5f6-1798111448661
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.createClinicalAnalysisTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createClinicalAnalysisTest(ClinicalAnalysisManagerTest.java:1580)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c11a90-0190-0007-0001-831da3a598d3-1804106089655
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.assignPermissions
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.assignPermissions(ClinicalAnalysisManagerTest.java:1489)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c12b0c-0190-0007-0001-38b261f87936-1808311468394
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.updateCustomPriorityTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateCustomPriorityTest(ClinicalAnalysisManagerTest.java:1654)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c136f2-0190-0007-0001-da897c9a01bc-1811363400904
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.testSearchAnnotation
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.testSearchAnnotation(ClinicalAnalysisManagerTest.java:3937)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c14e0b-0190-0007-0001-5b80b11f9bcc-1817276681942
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.updateClinicalAnalysisResponsible
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateClinicalAnalysisResponsible(ClinicalAnalysisManagerTest.java:381)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c159ef-0190-0007-0001-a628557fde60-1820344753242
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.updateClinicalAnalysisTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateClinicalAnalysisTest(ClinicalAnalysisManagerTest.java:1611)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c165e0-0190-0007-0001-fb2b2f5f6718-1823397638345
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.updateInterpretationTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateInterpretationTest(ClinicalAnalysisManagerTest.java:2202)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c171bd-0190-0007-0001-e95f557e7a92-1826414775017
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.sampleNotFoundInMember
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.sampleNotFoundInMember(ClinicalAnalysisManagerTest.java:3052)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c18170-0190-0007-0001-54c91a21c1aa-1830436770231
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 55 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithInterpretations
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithInterpretations(ClinicalAnalysisManagerTest.java:2701)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c18d77-0190-0007-0001-6713537b6394-1833513069733
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.searchByInternalAnnotationSetTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchByInternalAnnotationSetTest(ClinicalAnalysisManagerTest.java:3850)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c19d88-0190-0007-0001-516432a03eb1-1837618304063
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.updateClinicalAnalystsTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateClinicalAnalystsTest(ClinicalAnalysisManagerTest.java:292)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c1ad80-0190-0007-0001-5d61c44b290f-1841714859795
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.checkMoreThanOneSample
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.checkMoreThanOneSample(ClinicalAnalysisManagerTest.java:3082)
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$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c1bdf8-0190-0007-0001-42d9ef0eca17-1845924103834
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 55 more
github-actions / Surefire tests report
ClinicalAnalysisManagerTest.searchByDisorderTest
Error computing pedigree graph for family family
Raw output
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchByDisorderTest(ClinicalAnalysisManagerTest.java:2785)
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)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-e4c1ce02-0190-0007-0001-538097849890-1850044885646
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
... 56 more