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Prepare new development version 2.12.4.2-SNAPSHOT

Prepare new development version 2.12.4.2-SNAPSHOT #903

GitHub Actions / Surefire tests report failed May 9, 2024 in 0s

1401 tests run, 46 skipped, 80 failed.

Annotations

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

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalInterpretationAnalysisTest. 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUpCatalogManager(AbstractClinicalManagerTest.java:103)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUp(AbstractClinicalManagerTest.java:86)
	at org.opencb.opencga.analysis.clinical.ClinicalAnalysisUtilsTest.getClinicalTest(ClinicalAnalysisUtilsTest.java:52)
	at org.opencb.opencga.analysis.clinical.ClinicalInterpretationAnalysisTest.setUp(ClinicalInterpretationAnalysisTest.java:79)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.RunRules.evaluate(RunRules.java:20)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5d186260-018f-0007-0001-3121180e18c8-5769934924223
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 46 more

Check failure on line 58 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ExomiserInterpretationAnalysisTest. 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUpCatalogManager(AbstractClinicalManagerTest.java:103)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUp(AbstractClinicalManagerTest.java:86)
	at org.opencb.opencga.analysis.clinical.ClinicalAnalysisUtilsTest.getClinicalTest(ClinicalAnalysisUtilsTest.java:52)
	at org.opencb.opencga.analysis.clinical.exomiser.ExomiserInterpretationAnalysisTest.setUp(ExomiserInterpretationAnalysisTest.java:58)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.RunRules.evaluate(RunRules.java:20)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5d18ce95-018f-0007-0001-c6e61bd458f1-5797640343917
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 46 more

Check failure on line 138 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/manager/VariantCatalogQueryUtilsTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

VariantCatalogQueryUtilsTest. 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.analysis.variant.manager.VariantCatalogQueryUtilsTest.setUp(VariantCatalogQueryUtilsTest.java:138)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.RunRules.evaluate(RunRules.java:20)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5d1492ea-018f-0007-0001-1ead74d813be-5520113270470
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 41 more

Check failure on line 2666 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithEmptyInterpretations 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithEmptyInterpretations(ClinicalAnalysisManagerTest.java:2666)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdc61a8-018f-0007-0001-95dc3714a92a-1837776593074
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 2864 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.createClinicalAnalysisWithPanels 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createClinicalAnalysisWithPanels(ClinicalAnalysisManagerTest.java:2864)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdc7392-018f-0007-0001-8e1bf1d2f919-1842248266832
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 55 more

Check failure on line 2598 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.searchClinicalAnalysisByProband 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchClinicalAnalysisByProband(ClinicalAnalysisManagerTest.java:2598)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdc7f75-018f-0007-0001-3077be08d399-1845237756573
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 2390 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.updatePrimarySecondaryLockedInterpretationTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updatePrimarySecondaryLockedInterpretationTest(ClinicalAnalysisManagerTest.java:2390)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdc8b3f-018f-0007-0001-9cdef99e54df-1848265599652
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 1764 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.updateCustomConsentTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateCustomConsentTest(ClinicalAnalysisManagerTest.java:1764)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdcad66-018f-0007-0001-744b39ab889b-1856970703046
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 230 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.createAndTestStatusIdIsNotNull 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createAndTestStatusIdIsNotNull(ClinicalAnalysisManagerTest.java:230)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdcb870-018f-0007-0001-c8fc2a53c300-1859789774370
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 55 more

Check failure on line 1949 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.updateInterpretationFindingsTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateInterpretationFindingsTest(ClinicalAnalysisManagerTest.java:1949)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdcd015-018f-0007-0001-201548a76e00-1865871303212
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 2761 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.deleteLockedClinicalAnalysis 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteLockedClinicalAnalysis(ClinicalAnalysisManagerTest.java:2761)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdcdb20-018f-0007-0001-e4cdc0408170-1868675873854
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 2067 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.searchInterpretationVersion 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchInterpretationVersion(ClinicalAnalysisManagerTest.java:2067)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdce5fb-018f-0007-0001-5a493c128f04-1871447846760
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 1580 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.createClinicalAnalysisTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createClinicalAnalysisTest(ClinicalAnalysisManagerTest.java:1580)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdcfb6b-018f-0007-0001-610f6993bf29-1876935561177
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 1489 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.assignPermissions 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.assignPermissions(ClinicalAnalysisManagerTest.java:1489)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd0a4d-018f-0007-0001-0af962d7bf51-1880743450213
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 1654 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.updateCustomPriorityTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateCustomPriorityTest(ClinicalAnalysisManagerTest.java:1654)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd16ba-018f-0007-0001-6befa9314cf1-1883917860183
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 3937 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.testSearchAnnotation 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.testSearchAnnotation(ClinicalAnalysisManagerTest.java:3937)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd2b31-018f-0007-0001-bd85594f66d2-1889152381063
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 381 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.updateClinicalAnalysisResponsible 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateClinicalAnalysisResponsible(ClinicalAnalysisManagerTest.java:381)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd35f1-018f-0007-0001-9fd7e8262500-1891914816183
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 1611 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.updateClinicalAnalysisTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateClinicalAnalysisTest(ClinicalAnalysisManagerTest.java:1611)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd40bb-018f-0007-0001-9168308151d8-1894674428131
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 2202 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.updateInterpretationTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateInterpretationTest(ClinicalAnalysisManagerTest.java:2202)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd4b7c-018f-0007-0001-2cb6a842fbdb-1897429166207
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 3052 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.sampleNotFoundInMember 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.sampleNotFoundInMember(ClinicalAnalysisManagerTest.java:3052)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd59b1-018f-0007-0001-e6f891d51481-1901066680646
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 55 more

Check failure on line 2701 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithInterpretations 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.deleteClinicalAnalysisWithInterpretations(ClinicalAnalysisManagerTest.java:2701)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd64a4-018f-0007-0001-3350a60b1d88-1903863285044
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 3850 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.searchByInternalAnnotationSetTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchByInternalAnnotationSetTest(ClinicalAnalysisManagerTest.java:3850)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd7326-018f-0007-0001-ecb6f13a39a4-1907570280205
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 292 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.updateClinicalAnalystsTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.updateClinicalAnalystsTest(ClinicalAnalysisManagerTest.java:292)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd8170-018f-0007-0001-20a3f148b8c9-1911230018031
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more

Check failure on line 3082 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.checkMoreThanOneSample 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.checkMoreThanOneSample(ClinicalAnalysisManagerTest.java:3082)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd9084-018f-0007-0001-a7193282070d-1915094148754
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 55 more

Check failure on line 2785 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

ClinicalAnalysisManagerTest.searchByDisorderTest 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:214)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:130)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:125)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:123)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:100)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:121)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:279)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:224)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyFamily(ClinicalAnalysisManagerTest.java:188)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.createDummyEnvironment(ClinicalAnalysisManagerTest.java:200)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.searchByDisorderTest(ClinicalAnalysisManagerTest.java:2785)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-5cdd9ee0-018f-0007-0001-66127d3da52f-1918761596546
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:86)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:43)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:210)
	... 56 more
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