Login error causes Vivo to stop working

[juanlop...@gmail.com]

Hi!

I have an installation of VIVO 1.11 where in some cases when I login, the logs show this error:

2023-04-26 07:44:43,886 ERROR [Authenticate] Unexpected error in login process

java.lang.RuntimeException: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: java.lang.RuntimeException: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: org.apache.jena.tdb.transaction.TDBTransactionException: Exception after commit point - transaction did commit

        at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performAdd(RDFServiceGraph.java:139)

        at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.add(RDFServiceGraph.java:88)

        at org.apache.jena.graph.compose.MultiUnion.performAdd(MultiUnion.java:98)

        at org.apache.jena.graph.impl.GraphBase.add(GraphBase.java:181)

        at org.apache.jena.rdf.model.impl.ModelCom.add(ModelCom.java:1210)

        at org.apache.jena.rdf.model.impl.ModelCom.add(ModelCom.java:191)

        at edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao.updatePropertyLongValue(JenaBaseDao.java:379)

        at edu.cornell.mannlib.vitro.webapp.dao.jena.UserAccountsDaoJena.updateUserAccount(UserAccountsDaoJena.java:307)

        at edu.cornell.mannlib.vitro.webapp.dao.filtering.UserAccountsDaoFiltering.updateUserAccount(UserAccountsDaoFiltering.java:63)

        at edu.cornell.mannlib.vitro.webapp.controller.authenticate.BasicAuthenticator.recordLoginOnUserRecord(BasicAuthenticator.java:214)

        at edu.cornell.mannlib.vitro.webapp.controller.authenticate.BasicAuthenticator.recordLoginAgainstUserAccount(BasicAuthenticator.java:182)

        at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.transitionToLoggedIn(Authenticate.java:471)

        at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.processInputLoggingIn(Authenticate.java:371)

        at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.doPost(Authenticate.java:114)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:660)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:741)

        at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at org.apache.catalina.filters.ExpiresFilter.doFilter(ExpiresFilter.java:1230)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:111)

        at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:102)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:34)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:59)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:40)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:63)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.produceBasicResponse(CachingResponseFilter.java:321)

        at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.doFilter(CachingResponseFilter.java:120)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:64)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:36)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:41)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:66)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:199)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)

        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:494)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)

        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:651)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)

        at org.apache.coyote.ajp.AjpProcessor.service(AjpProcessor.java:394)

        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)

        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:754)

        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1385)

        at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)

        at java.lang.Thread.run(Thread.java:748)

Caused by: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: java.lang.RuntimeException: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: org.apache.jena.tdb.transaction.TDBTransactionException: Exception after commit point - transaction did commit

        at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel.changeSetUpdate(RDFServiceModel.java:117)

        at edu.cornell.mannlib.vitro.webapp.rdfservice.filter.LanguageFilteringRDFService.changeSetUpdate(LanguageFilteringRDFService.java:66)

        at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performAdd(RDFServiceGraph.java:137)

        ... 73 more

Caused by: java.lang.RuntimeException: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: org.apache.jena.tdb.transaction.TDBTransactionException: Exception after commit point - transaction did commit

        at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performAdd(RDFServiceGraph.java:139)

        at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.add(RDFServiceGraph.java:88)

        at org.apache.jena.rdf.model.impl.ModelCom.add(ModelCom.java:1210)

        at org.apache.jena.rdf.model.impl.ModelCom.add(ModelCom.java:1146)

        at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractModelDecorator.add(AbstractModelDecorator.java:739)

        at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.MemoryMappedModel$ModelSynchronizer.addedStatement(MemoryMappedModel.java:66)

        at org.apache.jena.rdf.model.impl.ModelListenerAdapter.notifyAddTriple(ModelListenerAdapter.java:53)

        at org.apache.jena.graph.impl.SimpleEventManager.notifyAddTriple(SimpleEventManager.java:98)

        at org.apache.jena.graph.impl.GraphBase.notifyAdd(GraphBase.java:124)

        at org.apache.jena.graph.impl.GraphBase.add(GraphBase.java:182)

        at org.apache.jena.graph.compose.MultiUnion.performAdd(MultiUnion.java:98)

        at java.util.ArrayList$Itr.forEachRemaining(ArrayList.java:899)

        at org.apache.jena.graph.GraphUtil.addIteratorWorkerDirect(GraphUtil.java:151)

        at org.apache.jena.graph.GraphUtil.addIteratorWorker(GraphUtil.java:145)

        at org.apache.jena.graph.GraphUtil.addInto(GraphUtil.java:139)

        at org.apache.jena.rdf.model.impl.ModelCom.add(ModelCom.java:225)

        at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractOntModelDecorator.add(AbstractOntModelDecorator.java:814)

        at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.BulkUpdatingOntModel.add(BulkUpdatingOntModel.java:79)

       at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena.operateOnModel(RDFServiceJena.java:114)

        at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel.changeSetUpdate(RDFServiceModel.java:97)

        ... 75 more

Caused by: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: org.apache.jena.tdb.transaction.TDBTransactionException: Exception after commit point - transaction did commit

        at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:90)

        at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle$UnclosableRDFService.changeSetUpdate(RDFServiceFactorySingle.java:75)

        at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.changeSetUpdate(LoggingRDFService.java:40)

        at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performAdd(RDFServiceGraph.java:137)

        ... 94 more

Caused by: org.apache.jena.tdb.transaction.TDBTransactionException: Exception after commit point - transaction did commit

        at org.apache.jena.tdb.transaction.Transaction.commit(Transaction.java:149)

        at org.apache.jena.tdb.transaction.DatasetGraphTxn.commit(DatasetGraphTxn.java:61)

        at org.apache.jena.tdb.transaction.DatasetGraphTransaction._commit(DatasetGraphTransaction.java:236)

        at org.apache.jena.sparql.core.DatasetGraphTrackActive.commit(DatasetGraphTrackActive.java:65)

        at org.apache.jena.sparql.core.DatasetImpl.commit(DatasetImpl.java:152)

        at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:80)

        ... 97 more

Caused by: org.apache.jena.tdb.transaction.TDBTransactionException: Checksum error reading from the Journal.

        at org.apache.jena.tdb.transaction.Journal._read(Journal.java:265)

        at org.apache.jena.tdb.transaction.Journal._readJournal(Journal.java:223)

        at org.apache.jena.tdb.transaction.Journal.access$100(Journal.java:46)

        at org.apache.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:290)

        at org.apache.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:275)

        at org.apache.jena.atlas.iterator.IteratorSlotted.hasNext(IteratorSlotted.java:66)

        at org.apache.jena.tdb.transaction.JournalControl.replay(JournalControl.java:243)

        at org.apache.jena.tdb.transaction.JournalControl.replay(JournalControl.java:230)

        at org.apache.jena.tdb.transaction.TransactionManager.processDelayedReplayQueue(TransactionManager.java:844)

        at org.apache.jena.tdb.transaction.TransactionManager.writerCommitsWorker(TransactionManager.java:781)

        at org.apache.jena.tdb.transaction.TransactionManager.access$500(TransactionManager.java:52)

        at org.apache.jena.tdb.transaction.TransactionManager$TSM_WriteBackEndTxn.writerCommits(TransactionManager.java:276)

        at org.apache.jena.tdb.transaction.TransactionManager.writerCommits(TransactionManager.java:1039)

        at org.apache.jena.tdb.transaction.TransactionManager.noteTxnCommit(TransactionManager.java:891)

        at org.apache.jena.tdb.transaction.TransactionManager.notifyCommit(TransactionManager.java:539)

        at org.apache.jena.tdb.transaction.Transaction.commit(Transaction.java:143)

        ... 102 more

and then Vivo hangs... in the past I've removed the journal.jrnl file from /vivo11and restarted tomcat (as mentioned in this post https://groups.google.com/g/vivo-tech/c/TE1LuDCrI5g/m/WiAB_jUcCAAJ)  but the error comes back from time to time.

Does anyone else has had this error?

Best regards,

Juan.