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Merge pull request #2473 from opencb/TASK-6345-2.12.6 #973

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Merge pull request #2473 from opencb/TASK-6345-2.12.6

Merge pull request #2473 from opencb/TASK-6345-2.12.6 #973

GitHub Actions / Surefire tests report failed Jul 11, 2024 in 0s

1419 tests run, 48 skipped, 81 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-a171f168-0190-0007-0001-3906234ca1a6-6992375781034
	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-a172689b-0190-0007-0001-8eb5c44e4f01-7022902431081
	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-a17144ec-0190-0007-0001-ce4a9cb2274c-6948114388185
	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-a12a360c-0190-0007-0001-b01058c3798d-2291595882551
	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-a12a5247-0190-0007-0001-34ab0f8e60d4-2298635710300
	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-a12a64b5-0190-0007-0001-e7142688b2a4-2303345489710
	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-a12a7729-0190-0007-0001-de09fe3f1b9d-2308164843293
	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-a12ab375-0190-0007-0001-ab4836c34b36-2323443283950
	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-a12ac64f-0190-0007-0001-b060b6b96bc9-2328255384335
	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-a12af024-0190-0007-0001-263f4a3f2edc-2338999869002
	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-a12b04c6-0190-0007-0001-79c786056a42-2344258359309
	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-a12b1645-0190-0007-0001-2884d3ac530c-2348727279058
	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-a12b3aa4-0190-0007-0001-811b0d0038d7-2358035138483
	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-a12b5385-0190-0007-0001-a299a9e7e27d-2364402816890
	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-a12b64dc-0190-0007-0001-d51c81bb4859-2368839717214
	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-a12b877b-0190-0007-0001-06642bfa42f2-2377728999300
	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-a12b9add-0190-0007-0001-90e9c1dc16b9-2382667633230
	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-a12bac29-0190-0007-0001-3de2ba964ceb-2387101822205
	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-a12bbdcc-0190-0007-0001-bcda3819c8d3-2391639476291
	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-a12bd68b-0190-0007-0001-007973e5b8d0-2397944479022
	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-a12be7f2-0190-0007-0001-0adb0aa9b89f-2402401922748
	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-a12c00d6-0190-0007-0001-2c05dcdcb3eb-2408765846486
	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-a12c1d30-0190-0007-0001-68eb178a8025-2416021202318
	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-a12c37d0-0190-0007-0001-b214bf61ded1-2422834519518
	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-a12c5041-0190-0007-0001-c457a26c9582-2429098786503
	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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