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analysis: use scratch dir as ephimeral directory, #TASK-6445 #2522

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analysis: use scratch dir as ephimeral directory, #TASK-6445

analysis: use scratch dir as ephimeral directory, #TASK-6445 #2522

GitHub Actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests failed Jan 31, 2025 in 0s

628 tests run, 7 skipped, 20 failed.

Annotations

Check failure on line 384 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

CatalogAuthorizationManagerTest.readProjectDeny 

Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.getArchiveCollection(AuthorizationMongoDBAdaptor.java:1207)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.update(AuthorizationMongoDBAdaptor.java:1161)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.removePermissions(AuthorizationMongoDBAdaptor.java:1121)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.lambda$resetMembersFromAllEntries$9(AuthorizationMongoDBAdaptor.java:783)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.resetMembersFromAllEntries(AuthorizationMongoDBAdaptor.java:771)
	at org.opencb.opencga.catalog.auth.authorization.CatalogAuthorizationManager.resetPermissionsFromAllEntities(CatalogAuthorizationManager.java:589)
	at org.opencb.opencga.catalog.managers.StudyManager.updateGroup(StudyManager.java:1236)
	at org.opencb.opencga.catalog.auth.authorization.CatalogAuthorizationManagerTest.readProjectDeny(CatalogAuthorizationManagerTest.java:384)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 404 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

CatalogAuthorizationManagerTest.readStudyDeny 

Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.getArchiveCollection(AuthorizationMongoDBAdaptor.java:1207)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.update(AuthorizationMongoDBAdaptor.java:1161)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.removePermissions(AuthorizationMongoDBAdaptor.java:1121)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.lambda$resetMembersFromAllEntries$9(AuthorizationMongoDBAdaptor.java:783)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.resetMembersFromAllEntries(AuthorizationMongoDBAdaptor.java:771)
	at org.opencb.opencga.catalog.auth.authorization.CatalogAuthorizationManager.resetPermissionsFromAllEntities(CatalogAuthorizationManager.java:589)
	at org.opencb.opencga.catalog.managers.StudyManager.updateGroup(StudyManager.java:1236)
	at org.opencb.opencga.catalog.auth.authorization.CatalogAuthorizationManagerTest.readStudyDeny(CatalogAuthorizationManagerTest.java:404)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 83 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/mongodb/AuthorizationMongoDBAdaptorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

AuthorizationMongoDBAdaptorTest.addSetGetAndRemoveAcls 

Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.getArchiveCollection(AuthorizationMongoDBAdaptor.java:1207)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.update(AuthorizationMongoDBAdaptor.java:1161)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.removePermissions(AuthorizationMongoDBAdaptor.java:1121)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.lambda$resetMembersFromAllEntries$9(AuthorizationMongoDBAdaptor.java:783)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.resetMembersFromAllEntries(AuthorizationMongoDBAdaptor.java:771)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptorTest.addSetGetAndRemoveAcls(AuthorizationMongoDBAdaptorTest.java:83)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 115 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

StudyMongoDBAdaptorTest.testRemoveFieldFromVariableSet 

No documents could be found to be updated
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: No documents could be found to be updated
	at org.opencb.opencga.catalog.db.mongodb.SnapshotVersionedMongoDBAdaptor.update(SnapshotVersionedMongoDBAdaptor.java:226)
	at org.opencb.opencga.catalog.db.mongodb.SnapshotVersionedMongoDBAdaptor.update(SnapshotVersionedMongoDBAdaptor.java:166)
	at org.opencb.opencga.catalog.db.mongodb.SampleMongoDBAdaptor.transactionalUpdate(SampleMongoDBAdaptor.java:468)
	at org.opencb.opencga.catalog.db.mongodb.AnnotationMongoDBAdaptor.lambda$removeAnnotationField$1(AnnotationMongoDBAdaptor.java:785)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.AnnotationMongoDBAdaptor.removeAnnotationField(AnnotationMongoDBAdaptor.java:784)
	at org.opencb.opencga.catalog.db.mongodb.StudyMongoDBAdaptor.removeFieldFromVariableSet(StudyMongoDBAdaptor.java:912)
	at org.opencb.opencga.catalog.db.mongodb.StudyMongoDBAdaptorTest.testRemoveFieldFromVariableSet(StudyMongoDBAdaptorTest.java:115)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 604 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

CatalogManagerTest.removeAllPermissionsToMember 

Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.getArchiveCollection(AuthorizationMongoDBAdaptor.java:1207)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.update(AuthorizationMongoDBAdaptor.java:1161)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.removePermissions(AuthorizationMongoDBAdaptor.java:1121)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.lambda$resetMembersFromAllEntries$9(AuthorizationMongoDBAdaptor.java:783)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.resetMembersFromAllEntries(AuthorizationMongoDBAdaptor.java:771)
	at org.opencb.opencga.catalog.auth.authorization.CatalogAuthorizationManager.resetPermissionsFromAllEntities(CatalogAuthorizationManager.java:589)
	at org.opencb.opencga.catalog.managers.StudyManager.updateGroup(StudyManager.java:1236)
	at org.opencb.opencga.catalog.managers.CatalogManagerTest.removeAllPermissionsToMember(CatalogManagerTest.java:604)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 656 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

CatalogManagerTest.removeUsersFromStudies 

Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.getArchiveCollection(AuthorizationMongoDBAdaptor.java:1207)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.update(AuthorizationMongoDBAdaptor.java:1161)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.removePermissions(AuthorizationMongoDBAdaptor.java:1121)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.lambda$resetMembersFromAllEntries$9(AuthorizationMongoDBAdaptor.java:783)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.resetMembersFromAllEntries(AuthorizationMongoDBAdaptor.java:771)
	at org.opencb.opencga.catalog.auth.authorization.CatalogAuthorizationManager.resetPermissionsFromAllEntities(CatalogAuthorizationManager.java:589)
	at org.opencb.opencga.catalog.managers.StudyManager.updateGroup(StudyManager.java:1236)
	at org.opencb.opencga.catalog.managers.CatalogManagerTest.removeUsersFromStudies(CatalogManagerTest.java:656)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 1716 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

CatalogManagerTest.testForceDeleteVariableSetWithAnnotations 

Could not delete VariableSet 'vs': No documents could be found to be updated
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Could not delete VariableSet 'vs': No documents could be found to be updated
	at org.opencb.opencga.catalog.db.mongodb.StudyMongoDBAdaptor.deleteVariableSet(StudyMongoDBAdaptor.java:1185)
	at org.opencb.opencga.catalog.managers.StudyManager.deleteVariableSet(StudyManager.java:1531)
	at org.opencb.opencga.catalog.managers.CatalogManagerTest.testForceDeleteVariableSetWithAnnotations(CatalogManagerTest.java:1716)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: org.opencb.opencga.catalog.exceptions.CatalogDBException: No documents could be found to be updated
	at org.opencb.opencga.catalog.db.mongodb.SnapshotVersionedMongoDBAdaptor.update(SnapshotVersionedMongoDBAdaptor.java:226)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.transactionalUpdate(FamilyMongoDBAdaptor.java:525)
	at org.opencb.opencga.catalog.db.mongodb.AnnotationMongoDBAdaptor.removeAllAnnotationSetsByVariableSetId(AnnotationMongoDBAdaptor.java:612)
	at org.opencb.opencga.catalog.db.mongodb.StudyMongoDBAdaptor.deleteAllAnnotationSetsByVariableSet(StudyMongoDBAdaptor.java:1213)
	at org.opencb.opencga.catalog.db.mongodb.StudyMongoDBAdaptor.lambda$deleteVariableSet$9(StudyMongoDBAdaptor.java:1170)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.StudyMongoDBAdaptor.deleteVariableSet(StudyMongoDBAdaptor.java:1168)
	... 48 more

Check failure on line 1599 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 hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

ClinicalAnalysisManagerTest.assignPermissions 

Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.getArchiveCollection(AuthorizationMongoDBAdaptor.java:1207)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.update(AuthorizationMongoDBAdaptor.java:1161)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.addToMembers(AuthorizationMongoDBAdaptor.java:693)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.lambda$addToMembers$5(AuthorizationMongoDBAdaptor.java:659)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.addToMembers(AuthorizationMongoDBAdaptor.java:654)
	at org.opencb.opencga.catalog.auth.authorization.CatalogAuthorizationManager.addAcls(CatalogAuthorizationManager.java:644)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManager.updateAcl(ClinicalAnalysisManager.java:2616)
	at org.opencb.opencga.catalog.managers.ClinicalAnalysisManagerTest.assignPermissions(ClinicalAnalysisManagerTest.java:1599)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 1065 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

FileManagerTest.testUnlinkFolder 

Could not unlink file 'myDirectory/A/'
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogException: Could not unlink file 'myDirectory/A/'
	at org.opencb.opencga.catalog.managers.FileManager.unlink(FileManager.java:1903)
	at org.opencb.opencga.catalog.managers.FileManagerTest.testUnlinkFolder(FileManagerTest.java:1065)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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: org.opencb.opencga.catalog.exceptions.CatalogDBException: Could not delete file myDirectory/A/: No documents could be found to be updated
	at org.opencb.opencga.catalog.db.mongodb.FileMongoDBAdaptor.delete(FileMongoDBAdaptor.java:1223)
	at org.opencb.opencga.catalog.managers.FileManager.unlink(FileManager.java:1985)
	at org.opencb.opencga.catalog.managers.FileManager.unlink(FileManager.java:1895)
	... 47 more

Check failure on line 468 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

FileManagerTest.associateAlignmentFilesTest 

Could not unlink file 'NA19600.chrom20.small.bam.bai'
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogException: Could not unlink file 'NA19600.chrom20.small.bam.bai'
	at org.opencb.opencga.catalog.managers.FileManager.unlink(FileManager.java:1903)
	at org.opencb.opencga.catalog.managers.FileManagerTest.associateAlignmentFilesTest(FileManagerTest.java:468)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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: org.opencb.opencga.catalog.exceptions.CatalogDBException: Could not delete file NA19600.chrom20.small.bam.bai: No documents could be found to be updated
	at org.opencb.opencga.catalog.db.mongodb.FileMongoDBAdaptor.delete(FileMongoDBAdaptor.java:1223)
	at org.opencb.opencga.catalog.managers.FileManager.unlink(FileManager.java:1985)
	at org.opencb.opencga.catalog.managers.FileManager.unlink(FileManager.java:1895)
	... 47 more

Check failure on line 2102 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

FileManagerTest.deleteFolderTest4 

Could not delete file folder/: No documents could be found to be updated
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogException: Could not delete file folder/: No documents could be found to be updated
	at org.opencb.opencga.catalog.managers.ResourceManager.endResult(ResourceManager.java:360)
	at org.opencb.opencga.catalog.managers.FileManager.delete(FileManager.java:1751)
	at org.opencb.opencga.catalog.managers.FileManager.delete(FileManager.java:1662)
	at org.opencb.opencga.catalog.managers.FileManagerTest.deleteFolderTest4(FileManagerTest.java:2102)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 2208 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

FileManagerTest.deleteFileUserInRelatedFilesTest 

Could not delete file data/test/folder/test_0.5K.txt: No documents could be found to be updated
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogException: Could not delete file data/test/folder/test_0.5K.txt: No documents could be found to be updated
	at org.opencb.opencga.catalog.managers.ResourceManager.endResult(ResourceManager.java:360)
	at org.opencb.opencga.catalog.managers.FileManager.delete(FileManager.java:1657)
	at org.opencb.opencga.catalog.managers.FileManager.delete(FileManager.java:1587)
	at org.opencb.opencga.catalog.managers.FileManagerTest.deleteFileUserInRelatedFilesTest(FileManagerTest.java:2208)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 1871 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

FileManagerTest.testDelete3 

Could not delete file data/: No documents could be found to be updated
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogException: Could not delete file data/: No documents could be found to be updated
	at org.opencb.opencga.catalog.managers.ResourceManager.endResult(ResourceManager.java:360)
	at org.opencb.opencga.catalog.managers.FileManager.delete(FileManager.java:1751)
	at org.opencb.opencga.catalog.managers.FileManager.delete(FileManager.java:1662)
	at org.opencb.opencga.catalog.managers.FileManagerTest.testDelete3(FileManagerTest.java:1871)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 804 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

FileManagerTest.testMoveFiles 

Could not update file A/B/C/: No documents could be found to be updated
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Could not update file A/B/C/: No documents could be found to be updated
	at org.opencb.opencga.catalog.db.mongodb.FileMongoDBAdaptor.update(FileMongoDBAdaptor.java:633)
	at org.opencb.opencga.catalog.managers.FileManager.move(FileManager.java:2431)
	at org.opencb.opencga.catalog.managers.FileManagerTest.testMoveFiles(FileManagerTest.java:804)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 1101 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

FileManagerTest.testUnlinkFile 

Could not unlink file 'myDirectory/data/test/folder/test_0.5K.txt'
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogException: Could not unlink file 'myDirectory/data/test/folder/test_0.5K.txt'
	at org.opencb.opencga.catalog.managers.FileManager.unlink(FileManager.java:1903)
	at org.opencb.opencga.catalog.managers.FileManagerTest.testUnlinkFile(FileManagerTest.java:1101)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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: org.opencb.opencga.catalog.exceptions.CatalogDBException: Could not delete file myDirectory/data/test/folder/test_0.5K.txt: No documents could be found to be updated
	at org.opencb.opencga.catalog.db.mongodb.FileMongoDBAdaptor.delete(FileMongoDBAdaptor.java:1223)
	at org.opencb.opencga.catalog.managers.FileManager.unlink(FileManager.java:1985)
	at org.opencb.opencga.catalog.managers.FileManager.unlink(FileManager.java:1895)
	... 47 more

Check failure on line 428 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/IndividualManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

IndividualManagerTest.changeIndividualIdTest2 

Could not update individual: No documents could be found to be updated
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Could not update individual: No documents could be found to be updated
	at org.opencb.opencga.catalog.db.mongodb.IndividualMongoDBAdaptor.update(IndividualMongoDBAdaptor.java:333)
	at org.opencb.opencga.catalog.managers.IndividualManager.update(IndividualManager.java:1161)
	at org.opencb.opencga.catalog.managers.IndividualManager.update(IndividualManager.java:944)
	at org.opencb.opencga.catalog.managers.IndividualManagerTest.changeIndividualIdTest2(IndividualManagerTest.java:428)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 78 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

ProjectManagerTest.searchSampleNoPermissions 

Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.getArchiveCollection(AuthorizationMongoDBAdaptor.java:1207)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.update(AuthorizationMongoDBAdaptor.java:1161)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.removePermissions(AuthorizationMongoDBAdaptor.java:1121)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.lambda$resetMembersFromAllEntries$9(AuthorizationMongoDBAdaptor.java:783)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.resetMembersFromAllEntries(AuthorizationMongoDBAdaptor.java:771)
	at org.opencb.opencga.catalog.auth.authorization.CatalogAuthorizationManager.resetPermissionsFromAllEntities(CatalogAuthorizationManager.java:589)
	at org.opencb.opencga.catalog.managers.StudyManager.updateGroup(StudyManager.java:1236)
	at org.opencb.opencga.catalog.managers.ProjectManagerTest.searchSampleNoPermissions(ProjectManagerTest.java:78)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 234 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/SampleManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

SampleManagerTest.testSampleVersioningWithWeirdId 

Error in identifier: 'test__Sa..mp--le' is not a valid id.
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogParameterException: Error in identifier: 'test__Sa..mp--le' is not a valid id.
	at org.opencb.opencga.catalog.utils.ParamUtils.checkIdentifier(ParamUtils.java:145)
	at org.opencb.opencga.catalog.managers.SampleManager.validateNewSample(SampleManager.java:168)
	at org.opencb.opencga.catalog.managers.SampleManager.create(SampleManager.java:248)
	at org.opencb.opencga.catalog.managers.SampleManagerTest.testSampleVersioningWithWeirdId(SampleManagerTest.java:234)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 209 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/UserManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

UserManagerTest.anonymousUserLoginTest 

Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Unexpected resource 'CLINICAL_ANALYSIS' parameter received.
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.getArchiveCollection(AuthorizationMongoDBAdaptor.java:1207)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.update(AuthorizationMongoDBAdaptor.java:1161)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.removePermissions(AuthorizationMongoDBAdaptor.java:1121)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.lambda$resetMembersFromAllEntries$9(AuthorizationMongoDBAdaptor.java:783)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	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:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.AuthorizationMongoDBAdaptor.resetMembersFromAllEntries(AuthorizationMongoDBAdaptor.java:771)
	at org.opencb.opencga.catalog.auth.authorization.CatalogAuthorizationManager.resetPermissionsFromAllEntities(CatalogAuthorizationManager.java:589)
	at org.opencb.opencga.catalog.managers.StudyManager.updateGroup(StudyManager.java:1236)
	at org.opencb.opencga.catalog.managers.UserManagerTest.anonymousUserLoginTest(UserManagerTest.java:209)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)

Check failure on line 126 in opencga-catalog/src/test/java/org/opencb/opencga/catalog/utils/FileScannerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report hdp3.1 opencga-catalog runShortTests,runMediumTests,runLongTests

FileScannerTest.testDeleteExisting 

Could not delete file data/test/folder/file1.txt: No documents could be found to be updated
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogException: Could not delete file data/test/folder/file1.txt: No documents could be found to be updated
	at org.opencb.opencga.catalog.managers.ResourceManager.endResult(ResourceManager.java:360)
	at org.opencb.opencga.catalog.managers.FileManager.delete(FileManager.java:1751)
	at org.opencb.opencga.catalog.managers.FileManager.delete(FileManager.java:1662)
	at org.opencb.opencga.catalog.utils.FileScanner.scan(FileScanner.java:278)
	at org.opencb.opencga.catalog.utils.FileScanner.scan(FileScanner.java:203)
	at org.opencb.opencga.catalog.utils.FileScannerTest.testDeleteExisting(FileScannerTest.java:126)
	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.TestWatcher$1.evaluate(TestWatcher.java:61)
	at org.junit.rules.ExpectedException$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.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)
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