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
--
Lingsoft - 30 years of Leading Language Management
www.lingsoft.fi
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Mikael Pesonen
System Engineer
e-mail: mikael.peso...@lingsoft.fi
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