Docker ext-tools manual deployer yml #745

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GitHub Actions / Surefire tests report failed Jul 26, 2023 in 0s

1320 tests run, 28 skipped, 74 failed.

Annotations

Check failure on line 79 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/ClinicalInterpretationAnalysisTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:95)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUp(AbstractClinicalManagerTest.java:78)
	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-94752368-0189-0007-0001-cd55a37cc9d5-8431429264689
	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:211)
	... 46 more

Check failure on line 49 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:95)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUp(AbstractClinicalManagerTest.java:78)
	at org.opencb.opencga.analysis.clinical.ClinicalAnalysisUtilsTest.getClinicalTest(ClinicalAnalysisUtilsTest.java:52)
	at org.opencb.opencga.analysis.clinical.exomiser.ExomiserInterpretationAnalysisTest.setUp(ExomiserInterpretationAnalysisTest.java:49)
	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-94748321-0189-0007-0001-ee15e35ae41c-8390443154830
	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:211)
	... 45 more

Check failure on line 137 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/manager/VariantCatalogQueryUtilsTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.analysis.variant.manager.VariantCatalogQueryUtilsTest.setUp(VariantCatalogQueryUtilsTest.java:137)
	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-9443868e-0189-0007-0001-bd9aeb23a9c1-5179653187329
	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:211)
	... 41 more

Check failure on line 2333 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithEmptyInterpretations(ClinicalAnalysisManagerTest.java:2333)
	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-94062dd1-0189-0007-0001-0b4ce398d8fe-1159675058814
	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:211)
	... 56 more

Check failure on line 2531 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createClinicalAnalysisWithPanels(ClinicalAnalysisManagerTest.java:2531)
	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-94064853-0189-0007-0001-ae07531c9059-1166345150128
	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:211)
	... 55 more

Check failure on line 2265 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchClinicalAnalysisByProband(ClinicalAnalysisManagerTest.java:2265)
	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-940658d5-0189-0007-0001-258f5f1414a6-1170504993469
	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:211)
	... 56 more

Check failure on line 2057 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updatePrimarySecondaryLockedInterpretationTest(ClinicalAnalysisManagerTest.java:2057)
	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-94066916-0189-0007-0001-017526fc782a-1174834611655
	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:211)
	... 56 more

Check failure on line 1431 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateCustomConsentTest(ClinicalAnalysisManagerTest.java:1431)
	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-94069bca-0189-0007-0001-66ac11e6414d-1187634252756
	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:211)
	... 56 more

Check failure on line 232 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createAndTestStatusIdIsNotNull(ClinicalAnalysisManagerTest.java:232)
	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-9406abb8-0189-0007-0001-0dca36fb6764-1191736397134
	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:211)
	... 55 more

Check failure on line 1616 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateInterpretationFindingsTest(ClinicalAnalysisManagerTest.java:1616)
	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-9406ccf9-0189-0007-0001-2d9d03de2cd5-1200203663971
	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:211)
	... 56 more

Check failure on line 2428 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteLockedClinicalAnalysis(ClinicalAnalysisManagerTest.java:2428)
	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-9406dca5-0189-0007-0001-0ca6fc494e2d-1204235581952
	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:211)
	... 56 more

Check failure on line 1734 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchInterpretationVersion(ClinicalAnalysisManagerTest.java:1734)
	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-9406ebb1-0189-0007-0001-10fc8eb3884b-1208020640490
	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:211)
	... 56 more

Check failure on line 1247 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createClinicalAnalysisTest(ClinicalAnalysisManagerTest.java:1247)
	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-940708b3-0189-0007-0001-087e7cc071d8-1215480024266
	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:211)
	... 56 more

Check failure on line 1156 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.assignPermissions(ClinicalAnalysisManagerTest.java:1156)
	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-94071dd9-0189-0007-0001-8e808159e308-1220844209011
	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:211)
	... 56 more

Check failure on line 1321 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateCustomPriorityTest(ClinicalAnalysisManagerTest.java:1321)
	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-94072cbe-0189-0007-0001-d4c4e6f2f7e5-1224657787594
	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:211)
	... 56 more

Check failure on line 1278 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateClinicalAnalysisTest(ClinicalAnalysisManagerTest.java:1278)
	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-94074926-0189-0007-0001-ec9da82c0487-1231928791224
	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:211)
	... 56 more

Check failure on line 1869 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateInterpretationTest(ClinicalAnalysisManagerTest.java:1869)
	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-940757ac-0189-0007-0001-063ec4d9edd7-1235663212752
	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:211)
	... 56 more

Check failure on line 2719 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.sampleNotFoundInMember(ClinicalAnalysisManagerTest.java:2719)
	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-94076b4d-0189-0007-0001-70cb139f0025-1240695426347
	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:211)
	... 55 more

Check failure on line 2368 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithInterpretations(ClinicalAnalysisManagerTest.java:2368)
	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-94077a1a-0189-0007-0001-14b34d911a63-1244514592215
	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:211)
	... 56 more

Check failure on line 2749 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.checkMoreThanOneSample(ClinicalAnalysisManagerTest.java:2749)
	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-94079f8b-0189-0007-0001-66d45ca05bc8-1254073234911
	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:211)
	... 55 more

Check failure on line 2452 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchByDisorderTest(ClinicalAnalysisManagerTest.java:2452)
	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-9407b426-0189-0007-0001-6d55e64c357a-1259326100265
	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:211)
	... 56 more

Check failure on line 1577 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

github-actions / Surefire tests report

ClinicalAnalysisManagerTest.clearSecondaryInterpretation

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.clearSecondaryInterpretation(ClinicalAnalysisManagerTest.java:1577)
	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-9407d536-0189-0007-0001-44fb1b2bc44b-1267799207520
	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:211)
	... 56 more

Check failure on line 382 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

github-actions / Surefire tests report

ClinicalAnalysisManagerTest.queryClinicalAnalysisByDate

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.queryClinicalAnalysisByDate(ClinicalAnalysisManagerTest.java:382)
	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-9407f09c-0189-0007-0001-cabbdf28e143-1274825133013
	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:211)
	... 56 more

Check failure on line 2316 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

github-actions / Surefire tests report

ClinicalAnalysisManagerTest.deleteClinicalAnalysisTest

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteClinicalAnalysisTest(ClinicalAnalysisManagerTest.java:2316)
	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-94080025-0189-0007-0001-245e5b776c49-1278821235022
	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:211)
	... 56 more

Check failure on line 1299 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

github-actions / Surefire tests report

ClinicalAnalysisManagerTest.updateCustomStatusTest

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:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$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:122)
	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:190)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:202)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateCustomStatusTest(ClinicalAnalysisManagerTest.java:1299)
	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-94080f53-0189-0007-0001-3ceca7cde19f-1282653111284
	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:211)
	... 56 more

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