Re: NodeTableTRDF/Read exception

Mon, 21 Mar 2022 11:43:45 -0700

The only time I have seen anything similar to this is on Android where something other process is messing about the files. TDB is not proof again other processes accessing the same files, including with shared network drives where different computers access the same filesystem. 

    Andy

On 21/03/2022 11:39, Mikael Pesonen wrote:
Got this again after few days of little usage after TDB2 was rebuilt from empty. Would you suggest this is hw error? No possibility that its Jena error? 

On 28/05/2021 17.25, Andy Seaborne wrote:



On 28/05/2021 14:59, Mikael Pesonen wrote:


I should try some older Jena/Fuseki version?


Yes.

Also
 - run on different hardware.
 - run multiple times
 - look at the data and see if anything unusual is in it.
 etc etc




On 28/05/2021 16.49, Andy Seaborne wrote:



On 28/05/2021 14:03, Mikael Pesonen wrote:
No this is the fresh db, started from empty today. And plenty of disk space. 

So it's repeatble.
With no Minimal, Verifiable, Complete Example, it'll have to be an on-site investigation. Try different versions. 

    Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:
Actually now it happened again. Same size, about 80MB of turtle, imported without warnings this time, but reading the graph fails with this exception. 

13:59:39 WARN  Fuseki          :: [44] RC = 500 : NodeTableTRDF/Read
org.apache.jena.tdb2.TDBException: NodeTableTRDF/Read
         at org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:52) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:206) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:131) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:52) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:113) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:108) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:53) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.IteratorWrapper.next(IteratorWrapper.java:36) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.dboe.transaction.txn.IteratorTxnTracker.next(IteratorTxnTracker.java:39) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.Iter.next(Iter.java:1072) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.mem.TrackingTripleIterator.next(TrackingTripleIterator.java:47) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.mem.TrackingTripleIterator.next(TrackingTripleIterator.java:31) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterTriplePattern$TripleMapper.hasNextBinding(QueryIterTriplePattern.java:145) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:74) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterBlockTriplesStar.hasNextBinding(QueryIterBlockTriplesStar.java:54) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterGroup$1.initializeIterator(QueryIterGroup.java:82) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.IteratorDelayedInitialization.init(IteratorDelayedInitialization.java:40) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.IteratorDelayedInitialization.hasNext(IteratorDelayedInitialization.java:50) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterPlainWrapper.hasNextBinding(QueryIterPlainWrapper.java:53) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:66) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at java.util.Iterator.forEachRemaining(Iterator.java:132) ~[?:?]          at org.apache.jena.atlas.data.DataBag.addAll(DataBag.java:94) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterSort$SortedBindingIterator.initializeIterator(QueryIterSort.java:87) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.IteratorDelayedInitialization.init(IteratorDelayedInitialization.java:40) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.IteratorDelayedInitialization.hasNext(IteratorDelayedInitialization.java:50) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterPlainWrapper.hasNextBinding(QueryIterPlainWrapper.java:53) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterConvert.hasNextBinding(QueryIterConvert.java:58) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterSlice.hasNextBinding(QueryIterSlice.java:76) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:38) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:38) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStream.java:74) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.ResultSetCheckCondition.hasNext(ResultSetCheckCondition.java:55) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.executeQuery(SPARQLQueryProcessor.java:324) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.execute(SPARQLQueryProcessor.java:273) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.executeBody(SPARQLQueryProcessor.java:233) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.execute(SPARQLQueryProcessor.java:213) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:58) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.execPost(SPARQLQueryProcessor.java:83) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.ActionProcessor.process(ActionProcessor.java:34) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.ActionBase.process(ActionBase.java:55) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.ActionExecLib.execAction(ActionExecLib.java:106) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.server.Dispatcher.dispatchAction(Dispatcher.java:118) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.server.Dispatcher.process(Dispatcher.java:110) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.server.Dispatcher.dispatch(Dispatcher.java:96) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:51) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:450) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) ~[fuseki-server.jar:3.17.0]          at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:284) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:247) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:602) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1612) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1582) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:716) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.Server.handle(Server.java:516) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:383) ~[fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:556) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:375) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:273) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:336) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:313) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:171) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:129) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:375) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:773) [fuseki-server.jar:3.17.0]          at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:905) [fuseki-server.jar:3.17.0] 
         at java.lang.Thread.run(Thread.java:832) [?:?]
Caused by: org.apache.thrift.protocol.TProtocolException: Unrecognized type 0          at org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:144) ~[fuseki-server.jar:3.17.0]          at org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:60) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:433) ~[fuseki-server.jar:3.17.0]          at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224) ~[fuseki-server.jar:3.17.0]          at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213) ~[fuseki-server.jar:3.17.0]          at org.apache.thrift.TUnion.read(TUnion.java:138) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:82) ~[fuseki-server.jar:3.17.0] 
         ... 189 more
13:59:39 INFO  Fuseki          :: [44] 500 Server Error (48 ms)


On 27/05/2021 18.39, Andy Seaborne wrote:
See the thread following from Harri's message "TDBException: NodeTableTRDF/Read (vol. 2)" 

    Andy


On 27/05/2021 15:56, Mikael Pesonen wrote:
Tried with the invalid data on fresh db and it didn't cause this exception. So root cause happened probably way earlier and is unknown. 

On 20/05/2021 14.10, Andy Seaborne wrote:

Please can we have a complete, minimal example.

On 19/05/2021 11:12, Mikael Pesonen wrote:
More info on this. When the causes of the two warnings are fixed, same data is imported correctly and everything works. So, when there are "too many" WARN level errors in importing data, the graph becomes corrupted. 

Unlikely to be related to how many.

You wrote:
>> but many warnings on invalid data

not two.  What is the problem data?

    Andy


On 18/05/2021 18.02, Andy Seaborne wrote:



On 18/05/2021 13:03, Mikael Pesonen wrote:
This occurred again on another server. There were no errors before this, but many warnings on invalid data, if that is related. Now we get this error on all operations.
12:57:42 WARN  Fuseki          :: [line: 149803, col: 81] Bad IRI: <mailto:"Finskas> Code: 4/UNWISE_CHARACTER in PATH: The character matches no grammar rules of URIs/IRIs. These characters are permitted in RDF URI References, XML system identifiers, and XML Schema anyURIs. 
...
14:48:28 WARN  Fuseki          :: [line: 475806, col: 80] Lexical form '' not valid for datatype XSD boolean 
...
Most likely different issues - these are to do with your data (being read in?).
They don't appear related but you could try a minimal test case based on that data.
Another thing to investigate is to look at the earlier log entries for [24] and see if you can spot the RDF terms that are affected by comparing them to other incidents. 

Maybe it is just one entry in the node table, or maybe not.

    Andy


14:52:06 WARN  Fuseki :: [24] RC = 500 : NodeTableTRDF/Read
org.apache.jena.tdb2.TDBException: NodeTableTRDF/Read
         at org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:52) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:206) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:131) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:52) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:65) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:112) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:108) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:53) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.IteratorWrapper.next(IteratorWrapper.java:36) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.dboe.transaction.txn.IteratorTxnTracker.next(IteratorTxnTracker.java:39) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.atlas.iterator.Iter.next(Iter.java:1072) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.mem.TrackingTripleIterator.next(TrackingTripleIterator.java:47) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.mem.TrackingTripleIterator.next(TrackingTripleIterator.java:31) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.iterator.QueryIterTriplePattern$TripleMapper.hasNextBinding(QueryIterTriplePattern.java:145) ~[fuseki-s erver.jar:3.17.0] 
...
         at org.apache.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStream.java:74) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.sparql.engine.ResultSetCheckCondition.hasNext(ResultSetCheckCondition.java:55) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.executeQuery(SPARQLQueryProcessor.java:324) ~[fuseki-server.jar:3.17.0]          at 

...
Caused by: org.apache.thrift.protocol.TProtocolException: Unrecognized type 0          at org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:144) ~[fuseki-server.jar:3.17.0]          at org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:60) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:433) ~[fuseki-server.jar:3.17.0]          at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224) ~[fuseki-server.jar:3.17.0]          at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213) ~[fuseki-server.jar:3.17.0]          at org.apache.thrift.TUnion.read(TUnion.java:138) ~[fuseki-server.jar:3.17.0]          at org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:82) ~[fuseki-server.jar:3.17.0] 
         ... 108 more
14:52:06 INFO  Fuseki          :: [24] 500 Server Error (12 ms) 



On 27/04/2021 13.22, Andy Seaborne wrote:



On 27/04/2021 09:59, Mikael Pesonen wrote:
That's our guess too, but would be nice to have some idea where to look for the cause. Does Jena/Fuseki handle disk full situations without corruption?
It should do (the transaction aborts) which is why I was asking.
Bulk loading, other than loader "basic" which is safe - depends exactly when it happens in the process i.e. no guarantees. 

    Andy




On 27/04/2021 11.56, Andy Seaborne wrote:

In the original message,
There was shortage of disk space, hope the db is not corrupted. 

What happened?
This is the only thing you've mentioned that relates to update.
Everything else is "read" and the fault occurred at an earlier time or its an environmental factor (one mentioned file access permissions e.g. another process is interfering with files).
Apr 12 12:30:55 solid java[22910]: [2021-04-12 12:30:55] Fuseki WARN [346] RC = 500 : a fault occurred in a recent unsafe memory access operation in compiled Java code Apr 12 12:30:55 solid java[22910]: at org.apache.jena.dboe.base.buffer.RecordBuffer.compare(RecordBuffer.java:192) ~[fuseki-server.jar:3.17.0]
so JDK ByteBuffer.get failed bu works almost always. It is likely to be an environmental factor (the file system, background process messing around, hardware issue). 

   Andy

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