error with first login for root on vivo 1.9.3 instance
Donald R Elsborg
Hello,
I’ve setup my vivo 1.9.3 instance on one of our redhat hosts and now have this error when I initially login.
The system allows me to login with the default rootPassword, but after I reset it I get a http 500 screen.
The vivo.all.log then has a lot of errors. I’ve pasted them below.
Environment is 1.9.3 with Openjdk 8
javac –version: javac 1.8.0_171
tomcat is running:
/usr/lib/jvm/jre-1.8.0/bin/java -version
openjdk version "1.8.0_171"
OpenJDK Runtime Environment (build 1.8.0_171-b10)
OpenJDK 64-Bit Server VM (build 25.171-b10, mixed mode)
Prior to the login attempt, other basic functions of the site worked fine.
Any help is appreciated.
Lot’s of java stack trace below.
Don
CU Boulder
2018-06-22 12:48:41,811 ERROR [JournalEntryType] Unknown type: 0
2018-06-22 12:48:41,813 ERROR [TDB] Exception during journal replay
org.apache.jena.atlas.lib.InternalErrorException: Unknown type: 0
at com.hp.hpl.jena.tdb.transaction.JournalEntryType.type(JournalEntryType.java:43)
at com.hp.hpl.jena.tdb.transaction.Journal._read(Journal.java:228)
at com.hp.hpl.jena.tdb.transaction.Journal._readJournal(Journal.java:197)
at com.hp.hpl.jena.tdb.transaction.Journal.access$100(Journal.java:48)
at com.hp.hpl.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:267)
at com.hp.hpl.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:248)
at org.apache.jena.atlas.iterator.IteratorSlotted.hasNext(IteratorSlotted.java:67)
at com.hp.hpl.jena.tdb.transaction.JournalControl.replay(JournalControl.java:245)
at com.hp.hpl.jena.tdb.transaction.JournalControl.replay(JournalControl.java:232)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.processDelayedReplayQueue(TransactionManager.java:559)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.writerCommitsWorker(TransactionManager.java:491)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.access$400(TransactionManager.java:47)
at com.hp.hpl.jena.tdb.transaction.TransactionManager$TSM_WriteBackEndTxn.writerCommits(TransactionManager.java:224)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.writerCommits(TransactionManager.java:784)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.noteTxnCommit(TransactionManager.java:619)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.notifyCommit(TransactionManager.java:415)
at com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:155)
at com.hp.hpl.jena.tdb.transaction.DatasetGraphTxn.commit(DatasetGraphTxn.java:44)
at com.hp.hpl.jena.tdb.transaction.DatasetGraphTransaction._commit(DatasetGraphTransaction.java:163)
at com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.commit(DatasetGraphTrackActive.java:53)
at com.hp.hpl.jena.sparql.core.DatasetImpl.commit(DatasetImpl.java:142)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:80)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle$UnclosableRDFService.changeSetUpdate(RDFServiceFactorySingle.java:75)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.changeSetUpdate(LoggingRDFService.java:40)
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performDelete(RDFServiceGraph.java:163)
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.delete(RDFServiceGraph.java:262)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.remove(ModelCom.java:346)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractModelDecorator.remove(AbstractModelDecorator.java:824)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.MemoryMappedModel$ModelSynchronizer.removedStatement(MemoryMappedModel.java:108)
at com.hp.hpl.jena.rdf.model.impl.ModelListenerAdapter.notifyDeleteTriple(ModelListenerAdapter.java:73)
at com.hp.hpl.jena.graph.impl.SimpleEventManager.notifyDeleteTriple(SimpleEventManager.java:131)
at com.hp.hpl.jena.graph.impl.GraphBase.notifyDelete(GraphBase.java:131)
at com.hp.hpl.jena.graph.impl.GraphBase.delete(GraphBase.java:226)
at com.hp.hpl.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:111)
at com.hp.hpl.jena.graph.impl.GraphBase.delete(GraphBase.java:225)
at com.hp.hpl.jena.graph.GraphUtil.remove(GraphUtil.java:308)
at com.hp.hpl.jena.graph.impl.GraphBase.remove(GraphBase.java:254)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.removeAll(ModelCom.java:386)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractOntModelDecorator.removeAll(AbstractOntModelDecorator.java:1104)
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:298)
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:111)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.transitionToLoggedIn(Authenticate.java:461)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.processInputChangePassword(Authenticate.java:410)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.doPost(Authenticate.java:115)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.filters.CorsFilter.handleSimpleCORS(CorsFilter.java:302)
at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:166)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:108)
at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:99)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:31)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:56)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:61)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.produceBasicResponse(CachingResponseFilter.java:319)
at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.doFilter(CachingResponseFilter.java:113)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:62)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:34)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:39)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:64)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:611)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
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)
2018-06-22 12:48:41,817 WARN [TDB] Exception after commit point : transaction commited but internal status not recorded properly
org.apache.jena.atlas.lib.InternalErrorException: Unknown type: 0
at com.hp.hpl.jena.tdb.transaction.JournalEntryType.type(JournalEntryType.java:43)
at com.hp.hpl.jena.tdb.transaction.Journal._read(Journal.java:228)
at com.hp.hpl.jena.tdb.transaction.Journal._readJournal(Journal.java:197)
at com.hp.hpl.jena.tdb.transaction.Journal.access$100(Journal.java:48)
at com.hp.hpl.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:267)
at com.hp.hpl.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:248)
at org.apache.jena.atlas.iterator.IteratorSlotted.hasNext(IteratorSlotted.java:67)
at com.hp.hpl.jena.tdb.transaction.JournalControl.replay(JournalControl.java:245)
at com.hp.hpl.jena.tdb.transaction.JournalControl.replay(JournalControl.java:232)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.processDelayedReplayQueue(TransactionManager.java:559)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.writerCommitsWorker(TransactionManager.java:491)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.access$400(TransactionManager.java:47)
at com.hp.hpl.jena.tdb.transaction.TransactionManager$TSM_WriteBackEndTxn.writerCommits(TransactionManager.java:224)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.writerCommits(TransactionManager.java:784)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.noteTxnCommit(TransactionManager.java:619)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.notifyCommit(TransactionManager.java:415)
at com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:155)
at com.hp.hpl.jena.tdb.transaction.DatasetGraphTxn.commit(DatasetGraphTxn.java:44)
at com.hp.hpl.jena.tdb.transaction.DatasetGraphTransaction._commit(DatasetGraphTransaction.java:163)
at com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.commit(DatasetGraphTrackActive.java:53)
at com.hp.hpl.jena.sparql.core.DatasetImpl.commit(DatasetImpl.java:142)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:80)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle$UnclosableRDFService.changeSetUpdate(RDFServiceFactorySingle.java:75)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.changeSetUpdate(LoggingRDFService.java:40)
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performDelete(RDFServiceGraph.java:163)
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.delete(RDFServiceGraph.java:262)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.remove(ModelCom.java:346)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractModelDecorator.remove(AbstractModelDecorator.java:824)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.MemoryMappedModel$ModelSynchronizer.removedStatement(MemoryMappedModel.java:108)
at com.hp.hpl.jena.rdf.model.impl.ModelListenerAdapter.notifyDeleteTriple(ModelListenerAdapter.java:73)
at com.hp.hpl.jena.graph.impl.SimpleEventManager.notifyDeleteTriple(SimpleEventManager.java:131)
at com.hp.hpl.jena.graph.impl.GraphBase.notifyDelete(GraphBase.java:131)
at com.hp.hpl.jena.graph.impl.GraphBase.delete(GraphBase.java:226)
at com.hp.hpl.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:111)
at com.hp.hpl.jena.graph.impl.GraphBase.delete(GraphBase.java:225)
at com.hp.hpl.jena.graph.GraphUtil.remove(GraphUtil.java:308)
at com.hp.hpl.jena.graph.impl.GraphBase.remove(GraphBase.java:254)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.removeAll(ModelCom.java:386)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractOntModelDecorator.removeAll(AbstractOntModelDecorator.java:1104)
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:298)
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:111)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.transitionToLoggedIn(Authenticate.java:461)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.processInputChangePassword(Authenticate.java:410)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.doPost(Authenticate.java:115)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.filters.CorsFilter.handleSimpleCORS(CorsFilter.java:302)
at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:166)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:108)
at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:99)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:31)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:56)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:61)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.produceBasicResponse(CachingResponseFilter.java:319)
at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.doFilter(CachingResponseFilter.java:113)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:62)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:34)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:39)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:64)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:611)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
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)
2018-06-22 12:48:41,820 ERROR [RDFServiceTDB] com.hp.hpl.jena.tdb.transaction.TDBTransactionException: Exc eption after commit point - transaction did commit
com.hp.hpl.jena.tdb.transaction.TDBTransactionException: Exc eption after commit point - transaction did commit
at com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:162)
at com.hp.hpl.jena.tdb.transaction.DatasetGraphTxn.commit(DatasetGraphTxn.java:44)
at com.hp.hpl.jena.tdb.transaction.DatasetGraphTransaction._commit(DatasetGraphTransaction.java:163)
at com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.commit(DatasetGraphTrackActive.java:53)
at com.hp.hpl.jena.sparql.core.DatasetImpl.commit(DatasetImpl.java:142)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:80)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle$UnclosableRDFService.changeSetUpdate(RDFServiceFactorySingle.java:75)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.changeSetUpdate(LoggingRDFService.java:40)
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performDelete(RDFServiceGraph.java:163)
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.delete(RDFServiceGraph.java:262)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.remove(ModelCom.java:346)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractModelDecorator.remove(AbstractModelDecorator.java:824)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.MemoryMappedModel$ModelSynchronizer.removedStatement(MemoryMappedModel.java:108)
at com.hp.hpl.jena.rdf.model.impl.ModelListenerAdapter.notifyDeleteTriple(ModelListenerAdapter.java:73)
at com.hp.hpl.jena.graph.impl.SimpleEventManager.notifyDeleteTriple(SimpleEventManager.java:131)
at com.hp.hpl.jena.graph.impl.GraphBase.notifyDelete(GraphBase.java:131)
at com.hp.hpl.jena.graph.impl.GraphBase.delete(GraphBase.java:226)
at com.hp.hpl.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:111)
at com.hp.hpl.jena.graph.impl.GraphBase.delete(GraphBase.java:225)
at com.hp.hpl.jena.graph.GraphUtil.remove(GraphUtil.java:308)
at com.hp.hpl.jena.graph.impl.GraphBase.remove(GraphBase.java:254)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.removeAll(ModelCom.java:386)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractOntModelDecorator.removeAll(AbstractOntModelDecorator.java:1104)
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:298)
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:111)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.transitionToLoggedIn(Authenticate.java:461)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.processInputChangePassword(Authenticate.java:410)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.doPost(Authenticate.java:115)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.filters.CorsFilter.handleSimpleCORS(CorsFilter.java:302)
at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:166)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:108)
at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:99)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:31)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:56)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:61)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.produceBasicResponse(CachingResponseFilter.java:319)
at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.doFilter(CachingResponseFilter.java:113)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:62)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:34)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:39)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:64)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:611)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
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: org.apache.jena.atlas.lib.InternalErrorException: Unknown type: 0
at com.hp.hpl.jena.tdb.transaction.JournalEntryType.type(JournalEntryType.java:43)
at com.hp.hpl.jena.tdb.transaction.Journal._read(Journal.java:228)
at com.hp.hpl.jena.tdb.transaction.Journal._readJournal(Journal.java:197)
at com.hp.hpl.jena.tdb.transaction.Journal.access$100(Journal.java:48)
at com.hp.hpl.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:267)
at com.hp.hpl.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:248)
at org.apache.jena.atlas.iterator.IteratorSlotted.hasNext(IteratorSlotted.java:67)
at com.hp.hpl.jena.tdb.transaction.JournalControl.replay(JournalControl.java:245)
at com.hp.hpl.jena.tdb.transaction.JournalControl.replay(JournalControl.java:232)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.processDelayedReplayQueue(TransactionManager.java:559)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.writerCommitsWorker(TransactionManager.java:491)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.access$400(TransactionManager.java:47)
at com.hp.hpl.jena.tdb.transaction.TransactionManager$TSM_WriteBackEndTxn.writerCommits(TransactionManager.java:224)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.writerCommits(TransactionManager.java:784)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.noteTxnCommit(TransactionManager.java:619)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.notifyCommit(TransactionManager.java:415)
at com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:155)
... 88 more
2018-06-22 12:48:41,823 ERROR [Authenticate] Unexpected error in login process
java.lang.RuntimeException: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: com.hp.hpl.jena.tdb.transaction.TDBTransactionException: Exc eption after commit point - transaction did commit
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performDelete(RDFServiceGraph.java:165)
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.delete(RDFServiceGraph.java:262)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.remove(ModelCom.java:346)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractModelDecorator.remove(AbstractModelDecorator.java:824)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.MemoryMappedModel$ModelSynchronizer.removedStatement(MemoryMappedModel.java:108)
at com.hp.hpl.jena.rdf.model.impl.ModelListenerAdapter.notifyDeleteTriple(ModelListenerAdapter.java:73)
at com.hp.hpl.jena.graph.impl.SimpleEventManager.notifyDeleteTriple(SimpleEventManager.java:131)
at com.hp.hpl.jena.graph.impl.GraphBase.notifyDelete(GraphBase.java:131)
at com.hp.hpl.jena.graph.impl.GraphBase.delete(GraphBase.java:226)
at com.hp.hpl.jena.graph.compose.MultiUnion.performDelete(MultiUnion.java:111)
at com.hp.hpl.jena.graph.impl.GraphBase.delete(GraphBase.java:225)
at com.hp.hpl.jena.graph.GraphUtil.remove(GraphUtil.java:308)
at com.hp.hpl.jena.graph.impl.GraphBase.remove(GraphBase.java:254)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.removeAll(ModelCom.java:386)
at edu.cornell.mannlib.vitro.webapp.rdfservice.adapters.AbstractOntModelDecorator.removeAll(AbstractOntModelDecorator.java:1104)
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:298)
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:111)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.transitionToLoggedIn(Authenticate.java:461)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.processInputChangePassword(Authenticate.java:410)
at edu.cornell.mannlib.vitro.webapp.controller.edit.Authenticate.doPost(Authenticate.java:115)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.filters.CorsFilter.handleSimpleCORS(CorsFilter.java:302)
at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:166)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:108)
at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:99)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:31)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:56)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:61)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.produceBasicResponse(CachingResponseFilter.java:319)
at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.doFilter(CachingResponseFilter.java:113)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:62)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:34)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:39)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:64)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:611)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
Caused by: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: com.hp.hpl.jena.tdb.transaction.TDBTransactionException: Exc eption after commit point - transaction did commit
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:90)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle$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.performDelete(RDFServiceGraph.java:163)
... 80 more
Caused by: com.hp.hpl.jena.tdb.transaction.TDBTransactionException: Exc eption after commit point - transaction did commit
at com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:162)
at com.hp.hpl.jena.tdb.transaction.DatasetGraphTxn.commit(DatasetGraphTxn.java:44)
at com.hp.hpl.jena.tdb.transaction.DatasetGraphTransaction._commit(DatasetGraphTransaction.java:163)
at com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.commit(DatasetGraphTrackActive.java:53)
at com.hp.hpl.jena.sparql.core.DatasetImpl.commit(DatasetImpl.java:142)
at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.changeSetUpdate(RDFServiceTDB.java:80)
... 83 more
Caused by: org.apache.jena.atlas.lib.InternalErrorException: Unknown type: 0
at com.hp.hpl.jena.tdb.transaction.JournalEntryType.type(JournalEntryType.java:43)
at com.hp.hpl.jena.tdb.transaction.Journal._read(Journal.java:228)
at com.hp.hpl.jena.tdb.transaction.Journal._readJournal(Journal.java:197)
at com.hp.hpl.jena.tdb.transaction.Journal.access$100(Journal.java:48)
at com.hp.hpl.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:267)
at com.hp.hpl.jena.tdb.transaction.Journal$IteratorEntries.moveToNext(Journal.java:248)
at org.apache.jena.atlas.iterator.IteratorSlotted.hasNext(IteratorSlotted.java:67)
at com.hp.hpl.jena.tdb.transaction.JournalControl.replay(JournalControl.java:245)
at com.hp.hpl.jena.tdb.transaction.JournalControl.replay(JournalControl.java:232)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.processDelayedReplayQueue(TransactionManager.java:559)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.writerCommitsWorker(TransactionManager.java:491)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.access$400(TransactionManager.java:47)
at com.hp.hpl.jena.tdb.transaction.TransactionManager$TSM_WriteBackEndTxn.writerCommits(TransactionManager.java:224)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.writerCommits(TransactionManager.java:784)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.noteTxnCommit(TransactionManager.java:619)
at com.hp.hpl.jena.tdb.transaction.TransactionManager.notifyCommit(TransactionManager.java:415)
at com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:155)
... 88 more
Triggs, Graham
Hi Don,
That’s a TDB (<vivo_home/tdbModels) error. Is this an entirely clean instance that you are deploying, or have you copied an existing home directory (and content store)?
If you’ve taken a copy of an existing home directory, and done so whilst VIVO is running, that’s not going to work.
Regards,
Graham
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Donald R Elsborg
I reverted to trying a fresh clean install, and it’s still not working.
Just as an aside, it’s working on our dev instance.
Don
To view this discussion on the web visit https://groups.google.com/d/msgid/vivo-tech/0CBF6BD9529827458C194C3AAD14A55301EC4E57%40smsx2003.tib.tibub.de.
Huda J. Khan
Sent: Friday, June 22, 2018 4:47:42 PM
Donald R Elsborg
Huda, thanks for this tip but it looks like all the files in tdbModels and the directory are owned and grouped by tomcat. So not sure what to even change this to. Listing below:
elsborg@prometheus-dev:/usr/local/vivo/vivo-cub-dev/vdata/tdbModels$ ls -altr
total 932
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 SPO.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 SPO.dat
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 POS.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 POS.dat
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 OSP.dat
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 OSP.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 prefixIdx.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 prefixIdx.dat
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 prefix2id.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 prefix2id.dat
-rw-r--r-- 1 tomcat tomcat 0 Jun 25 17:23 prefixes.dat
-rw-r--r-- 1 tomcat tomcat 0 Jun 25 17:23 prefixes.dat-jrnl
drwxr-xr-x 2 tomcat tomcat 4096 Jun 25 17:23 .
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 node2id.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 GPOS.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 GOSP.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 POSG.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 OSPG.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 GPOS.dat
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 GOSP.dat
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 OSPG.dat
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 SPOG.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 SPOG.dat
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 GSPO.idn
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 GSPO.dat
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:23 POSG.dat
-rw-r--r-- 1 tomcat tomcat 0 Jun 25 17:26 nodes.dat-jrnl
-rw-r--r-- 1 tomcat tomcat 8388608 Jun 25 17:26 node2id.dat
-rw-r--r-- 1 tomcat tomcat 51567 Jun 25 17:26 nodes.dat
-rw-r--r-- 1 tomcat tomcat 575060 Jun 25 17:26 journal.jrnl
drwxrwxr-x 9 elsborg facstaff 4096 Jun 25 17:31 ..
I found that when I deployed to a different tomcat instance, it worked for a bit.
Then I made a change to the PropertyConfig.n3 file – which I noticed was moved to firsttime from everytime several years ago, not sure why?
After that change I destroyed the tdbModels and let VIVO rebuild it, because the changes are in the firsttime graph.
After that this error occurred again.
I have destroyed and re-installed our full 3 tier source and re-cloned multiple times. I have tried doing this against just the VIVO source. All to no-avail.
I also tried removing all files under the tomcat webapps and work directories thinking something is cached somewhere.
This problem still exists even after a system reboot.
So it seems that once this happens to a tomcat instance it persists somehow after numerous rebuilds.
Does anybody know if tomcat and/or tdb caches information somewhere else?
Don
To view this discussion on the web visit https://groups.google.com/d/msgid/vivo-tech/BLUPR04MB165E4C96DF021DACBA9EEC0BD740%40BLUPR04MB165.namprd04.prod.outlook.com.
Alex Viggio
Second Don's thanks for the replies!
I was looking at the Java code in
Vitro/api/src/main/java/edu/cornell/mannlib/vitro/webapp/servlet/setup/RDFFilesLoader.java
and noticed that the loadFirstTimeFiles() and loadEveryTimeFiles()
code is slightly different.
loadEveryTimeFiles() creates a local OntModel object, then loops
through and reads the ontology files into that temp object using the
simple Model.read() method, and finally adds that object to the passed
in Model using the OntModel.addSubModel() method. The Jena javadoc for
that addSubModel() method indicates that it will "cause the associated
inference engine (if any) to update." Why does loadFirstTimeFiles()
not call addSubModel()?
I'm guessing this difference is 100% intentional, but the code isn't
commented to explain why. Don't know that there is an "associated
inference engine" at run-time, but I was suspicious based on the issue
seeming to crop up after Don had moved some RDF files from the
everytime to firsttime directories.
Very curious to track down the root cause given Don's reproduced this
TDB error on a RedHat Linux (RHEL) VM now in addition to a physical
RHEL server. As he explains, we seem to be stuck in a broken state and
not clear how to roll things back so TDB works again.
I followed along as Don cleared files from vdata and the Tomcat webapp
and work directories, and the RHEL VM was rebooted. With a clean VIVO
1.9.3 Maven build, the original TDB error persisted which is why we're
wondering if the TDB v0.10.0 library (or some other Jena component) is
maintaining state in another location on the server than vdata, or
Tomcat webapp or work dirs. I searched the Jena JIRA instance for the
error ("TDBTransactionException") and there are some references, but
nothing that seems to map to our situation. Not sure if this JIRA
instance goes back to 2012/2013 when 0.10.0 was in play.
Not ruling out we've overlooked something as there are lots of moving
parts, but also aware that 1.9.3 is using an old version of Jena+TDB
(looks like 0.10.0 was the first GA release of TDB after the 0.9,x
"incubating" versions). Was scanning release notes for TDB versions
after 0.10.0, and there are clearly bug fixes. Unfortunately the Jena
project relies on a JIRA "feature" to generate release notes which are
pretty spotty to non-existent for many of the releases between 0.10.0
and the latest 3.7.0 TDB releases (TDB1 and TDB2 variants).
Another question -- has anyone been able to configure VIVO to use SDB
for the app config triples? We tried making this config change
(hasConfigurationTripleSource in /vdata/config/applicationSetup.n3) at
one point yesterday, but errors flew on Tomcat startup so we rolled
the config back to TDB.
Any other TDB debugging suggestions or thoughts are appreciated.
- Alex
Donald R Elsborg
I wanted to share how we solved this issue.
We stopped tomcat, then deleted the journal.jrnl file, then started tomcat.
After that we were able to login with the initial rootPassword and then followed the prompts to change the password.
The root cause/ business case for this is that we needed to change the PropertyConfig.n3 file in the display/firsttime directory. Note that this file used to be in display/everytime directory but was moved since version 1.7
So in order to change a displayname or a propertygroup assignment, I will have to shutdown tomcat, remove the tdbModels directory , and then restart it which will force VIVO to re-read the firsttime files.
We want to make our changes in the files because we configure our VIVO via github and not via the GUI.
Don
> -----Original Message-----
> From: vivo...@googlegroups.com [mailto:vivo...@googlegroups.com]
> On Behalf Of Alex Viggio
> Sent: Tuesday, June 26, 2018 9:21 AM
> To: vivo...@googlegroups.com
> Subject: Re: [vivo-tech] error with first login for root on vivo 1.9.3 instance
>
> >
> > at java.lang.Thread.run(Thread.java:748)
> >
> > 2018-06-22 12:48:41,820 ERROR [RDFServiceTDB]
> > com.hp.hpl.jena.tdb.transaction.TDBTransactionException: Exc eption after
> > commit point - transaction did commit
> >
> > com.hp.hpl.jena.tdb.transaction.TDBTransactionException: Exc eption after
> > commit point - transaction did commit
> >
> > at
> > com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:162)
> >
> > at
> >
> com.hp.hpl.jena.tdb.transaction.DatasetGraphTxn.commit(DatasetGraphTxn.
> java:44)
> >
> > at
> >
> com.hp.hpl.jena.tdb.transaction.DatasetGraphTransaction._commit(Dataset
> GraphTransaction.java:163)
> >
> > at
> >
> com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.commit(DatasetGraph
> >
> > at java.lang.Thread.run(Thread.java:748)
> >
> > Caused by: org.apache.jena.atlas.lib.InternalErrorException: Unknown
> type: 0
> >
> > at
> >
> com.hp.hpl.jena.tdb.transaction.JournalEntryType.type(JournalEntryType.jav
> >
> > at
> > com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:155)
> >
> > ... 88 more
> >
> > 2018-06-22 12:48:41,823 ERROR [Authenticate] Unexpected error in login
> > process
> >
> > java.lang.RuntimeException:
> > edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException:
> > com.hp.hpl.jena.tdb.transaction.TDBTransactionException: Exc eption after
> > commit point - transaction did commit
> >
> > at
> >
> edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.performDelete(
> RDFServiceGraph.java:165)
> >
> > at
> >
> edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceGraph.delete(RDFServi
> >
> > at
> > com.hp.hpl.jena.sparql.core.DatasetImpl.commit(DatasetImpl.java:142)
> >
> > at
> >
> edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB.ch
> >
> > ... 83 more
> >
> > Caused by: org.apache.jena.atlas.lib.InternalErrorException: Unknown
> type: 0
> >
> > at
> >
> com.hp.hpl.jena.tdb.transaction.JournalEntryType.type(JournalEntryType.jav
> > For more options, visit https://groups.google.com/d/optout.
> >
> > --
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> > To post to this group, send email to vivo...@googlegroups.com.
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> > To view this discussion on the web visit
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> >
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> >
> > For more options, visit https://groups.google.com/d/optout.
>
> --
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