brianjlowe
commented
3 months ago Hi Elvis,
It looks like something went wrong internally in the triple store that holds the user accounts; this is stored in the ’tdbModels’ subdirectory of your VIVO home directory. Perhaps it somehow didn’t shut down cleanly during one of the upgrades. When you say the error occurs again when you reinstall from zero, is that with an empty database (i.e. only the default root account), or are you reusing the existing home directory?
The first thing I would suggest to try is to (1) shut down VIVO, (2) make a backup copy of the tdbModels directory, (3) delete the journal.jrnl file in that directory, and (4) restart VIVO.
Let’s hope that leads to some improvement; please let us know how it goes.
ElvisAravena
Dear All,
Along with greeting, I have been working with the different versions of ViVO, starting from VIVO-1.11, VIVO-1.12 and VIVO-1.13 currently. In all of them I have carried out the updates without problems. But when I upgraded from VIVO-1.13 to VIVO-1.14, a problem arose when performing user authentication, that is, it did not perform authentication and did not change the password. I tried performing a clean installation from 0, on different machines and the problem repeats itself, again it does not allow the password to be changed.
Screenshots
Review log: vivo-all.log 2024-07-18 11:49:00,262 WARN [TDB] Exception after commit point : transaction commited but internal status not recorded properly 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) at org.apache.jena.tdb.transaction.DatasetGraphTxn.commit(DatasetGraphTxn.java:61) at org.apache.jena.tdb.transaction.DatasetGraphTransaction.commit(DatasetGraphTransaction.java:200) 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:84) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle$UnclosableRDFService.changeSetUpdate(RDFServiceFactorySingle.java:76) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.changeSetUpdate(LoggingRDFService.java:41) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performDelete(RDFServiceGraph.java:160) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.delete(RDFServiceGraph.java:259) at org.apache.jena.rdf.model.impl.ModelCom.remove(ModelCom.java:392) at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractModelDecorator.remove(AbstractModelDecorator.java:849) at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.MemoryMappedModel$ModelSynchronizer.removedStatement(MemoryMappedModel.java:108) at org.apache.jena.rdf.model.impl.ModelListenerAdapter.notifyDeleteTriple(ModelListenerAdapter.java:73) at org.apache.jena.graph.impl.SimpleEventManager.notifyDeleteTriple(SimpleEventManager.java:133) at org.apache.jena.graph.impl.GraphBase.notifyDelete(GraphBase.java:134) at org.apache.jena.graph.impl.GraphBase.delete(GraphBase.java:208) at org.apache.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:112) at org.apache.jena.graph.impl.GraphBase.delete(GraphBase.java:207) at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractGraphDecorator.delete(AbstractGraphDecorator.java:68) at org.apache.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:112) at org.apache.jena.graph.impl.GraphBase.delete(GraphBase.java:207) at org.apache.jena.graph.GraphUtil.remove(GraphUtil.java:221) at org.apache.jena.graph.impl.GraphBase.remove(GraphBase.java:236) at org.apache.jena.rdf.model.impl.ModelCom.removeAll(ModelCom.java:427) at edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao.updatePropertyBooleanValue(JenaBaseDao.java:221) at edu.cornell.mannlib.vitro.webapp.dao.jena.UserAccountsDaoJena.updateUserAccount(UserAccountsDaoJena.java:306) at edu.cornell.mannlib.vitro.webapp.dao.filtering.UserAccountsDaoFiltering.updateUserAccount(UserAccountsDaoFiltering.java:63) at edu.cornell.mannlib.vitro.webapp.controller.authenticate.BasicAuthenticator.recordNewPassword(BasicAuthenticator.java:138) at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.transitionToLoggedIn(Authenticate.java:483) at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.processInputChangePassword(Authenticate.java:433) at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.doPost(Authenticate.java:117) at javax.servlet.http.HttpServlet.service(HttpServlet.java:681) at javax.servlet.http.HttpServlet.service(HttpServlet.java:764) at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:232) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at org.apache.catalina.filters.ExpiresFilter.doFilter(ExpiresFilter.java:1230) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:112) at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:103) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:34) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:59) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:40) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) 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:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:64) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:36) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:41) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:66) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:544) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:143) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:698) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:364) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:624) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:831) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1651) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.base/java.lang.Thread.run(Thread.java:829) 2024-07-18 11:49:00,263 ERROR [RDFServiceTDB] org.apache.jena.tdb.transaction.TDBTransactionException: Transaction has already committed or aborted org.apache.jena.tdb.transaction.TDBTransactionException: Transaction has already committed or aborted at org.apache.jena.tdb.transaction.Transaction.abort(Transaction.java:305) at org.apache.jena.tdb.transaction.DatasetGraphTxn.abort(DatasetGraphTxn.java:66) at org.apache.jena.tdb.transaction.DatasetGraphTransaction.abort(DatasetGraphTransaction.java:208) at org.apache.jena.sparql.core.DatasetImpl.abort(DatasetImpl.java:158) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:88) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle$UnclosableRDFService.changeSetUpdate(RDFServiceFactorySingle.java:76) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.changeSetUpdate(LoggingRDFService.java:41) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performDelete(RDFServiceGraph.java:160) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.delete(RDFServiceGraph.java:259) at org.apache.jena.rdf.model.impl.ModelCom.remove(ModelCom.java:392) at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractModelDecorator.remove(AbstractModelDecorator.java:849) at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.MemoryMappedModel$ModelSynchronizer.removedStatement(MemoryMappedModel.java:108) at org.apache.jena.rdf.model.impl.ModelListenerAdapter.notifyDeleteTriple(ModelListenerAdapter.java:73) at org.apache.jena.graph.impl.SimpleEventManager.notifyDeleteTriple(SimpleEventManager.java:133) at org.apache.jena.graph.impl.GraphBase.notifyDelete(GraphBase.java:134) at org.apache.jena.graph.impl.GraphBase.delete(GraphBase.java:208) at org.apache.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:112) at org.apache.jena.graph.impl.GraphBase.delete(GraphBase.java:207) at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractGraphDecorator.delete(AbstractGraphDecorator.java:68) at org.apache.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:112) at org.apache.jena.graph.impl.GraphBase.delete(GraphBase.java:207) at org.apache.jena.graph.GraphUtil.remove(GraphUtil.java:221) at org.apache.jena.graph.impl.GraphBase.remove(GraphBase.java:236) at org.apache.jena.rdf.model.impl.ModelCom.removeAll(ModelCom.java:427) at edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao.updatePropertyBooleanValue(JenaBaseDao.java:221) at edu.cornell.mannlib.vitro.webapp.dao.jena.UserAccountsDaoJena.updateUserAccount(UserAccountsDaoJena.java:306) at edu.cornell.mannlib.vitro.webapp.dao.filtering.UserAccountsDaoFiltering.updateUserAccount(UserAccountsDaoFiltering.java:63) at edu.cornell.mannlib.vitro.webapp.controller.authenticate.BasicAuthenticator.recordNewPassword(BasicAuthenticator.java:138) at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.transitionToLoggedIn(Authenticate.java:483) at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.processInputChangePassword(Authenticate.java:433) at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.doPost(Authenticate.java:117) at javax.servlet.http.HttpServlet.service(HttpServlet.java:681) at javax.servlet.http.HttpServlet.service(HttpServlet.java:764) at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:232) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at org.apache.catalina.filters.ExpiresFilter.doFilter(ExpiresFilter.java:1230) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:112) at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:103) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:34) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:59) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:40) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) 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:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:64) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:36) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:41) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:66) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:544) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:143) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:698) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:364) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:624) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:831) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1651) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.base/java.lang.Thread.run(Thread.java:829) 2024-07-18 11:49:00,264 ERROR [Authenticate] Unexpected error in login process java.lang.RuntimeException: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: org.apache.jena.tdb.transaction.TDBTransactionException: Transaction has already committed or aborted at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performDelete(RDFServiceGraph.java:162) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.delete(RDFServiceGraph.java:259) at org.apache.jena.rdf.model.impl.ModelCom.remove(ModelCom.java:392) at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractModelDecorator.remove(AbstractModelDecorator.java:849) at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.MemoryMappedModel$ModelSynchronizer.removedStatement(MemoryMappedModel.java:108) at org.apache.jena.rdf.model.impl.ModelListenerAdapter.notifyDeleteTriple(ModelListenerAdapter.java:73) at org.apache.jena.graph.impl.SimpleEventManager.notifyDeleteTriple(SimpleEventManager.java:133) at org.apache.jena.graph.impl.GraphBase.notifyDelete(GraphBase.java:134) at org.apache.jena.graph.impl.GraphBase.delete(GraphBase.java:208) at org.apache.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:112) at org.apache.jena.graph.impl.GraphBase.delete(GraphBase.java:207) at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractGraphDecorator.delete(AbstractGraphDecorator.java:68) at org.apache.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:112) at org.apache.jena.graph.impl.GraphBase.delete(GraphBase.java:207) at org.apache.jena.graph.GraphUtil.remove(GraphUtil.java:221) at org.apache.jena.graph.impl.GraphBase.remove(GraphBase.java:236) at org.apache.jena.rdf.model.impl.ModelCom.removeAll(ModelCom.java:427) at edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao.updatePropertyBooleanValue(JenaBaseDao.java:221) at edu.cornell.mannlib.vitro.webapp.dao.jena.UserAccountsDaoJena.updateUserAccount(UserAccountsDaoJena.java:306) at edu.cornell.mannlib.vitro.webapp.dao.filtering.UserAccountsDaoFiltering.updateUserAccount(UserAccountsDaoFiltering.java:63) at edu.cornell.mannlib.vitro.webapp.controller.authenticate.BasicAuthenticator.recordNewPassword(BasicAuthenticator.java:138) at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.transitionToLoggedIn(Authenticate.java:483) at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.processInputChangePassword(Authenticate.java:433) at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.doPost(Authenticate.java:117) at javax.servlet.http.HttpServlet.service(HttpServlet.java:681) at javax.servlet.http.HttpServlet.service(HttpServlet.java:764) at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:232) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at org.apache.catalina.filters.ExpiresFilter.doFilter(ExpiresFilter.java:1230) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:112) at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:103) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:34) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:59) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:40) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:63) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) 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:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:64) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:36) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:41) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:66) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:194) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:167) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:544) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:143) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:698) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:364) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:624) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:831) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1651) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: org.apache.jena.tdb.transaction.TDBTransactionException: Transaction has already committed or aborted at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:100) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle$UnclosableRDFService.changeSetUpdate(RDFServiceFactorySingle.java:76) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.changeSetUpdate(LoggingRDFService.java:41) at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performDelete(RDFServiceGraph.java:160) ... 83 more Caused by: org.apache.jena.tdb.transaction.TDBTransactionException: Transaction has already committed or aborted at org.apache.jena.tdb.transaction.Transaction.abort(Transaction.java:305) at org.apache.jena.tdb.transaction.DatasetGraphTxn.abort(DatasetGraphTxn.java:66) at org.apache.jena.tdb.transaction.DatasetGraphTransaction.abort(DatasetGraphTransaction.java:208) at org.apache.jena.sparql.core.DatasetImpl.abort(DatasetImpl.java:158) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:88) ... 86 more
Environment (please complete the following information): Operating System: CentOS Linux 8 CPE OS Name: cpe:/o:centos:centos:8 Kernel: Linux 4.18.0-348.7.1.el8_5.x86_64 Architecture: x86-64
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