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Posted to dev@jena.apache.org by "Andy Seaborne (JIRA)" <ji...@apache.org> on 2019/07/07 15:52:00 UTC
[jira] [Resolved] (JENA-1719) Fuseki with TDB2 using RDFS inference
throws exception on queries
[ https://issues.apache.org/jira/browse/JENA-1719?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Andy Seaborne resolved JENA-1719.
---------------------------------
Resolution: Fixed
Fix Version/s: Jena 3.13.0
> Fuseki with TDB2 using RDFS inference throws exception on queries
> -----------------------------------------------------------------
>
> Key: JENA-1719
> URL: https://issues.apache.org/jira/browse/JENA-1719
> Project: Apache Jena
> Issue Type: Bug
> Affects Versions: Jena 3.10.0, Jena 3.11.0
> Reporter: Mike Welch
> Assignee: Dave Reynolds
> Priority: Major
> Fix For: Jena 3.13.0
>
> Attachments: data.nt, example.owl, example.ttl
>
> Time Spent: 50m
> Remaining Estimate: 0h
>
> Configuring an InfModel with an RDFS reasoner and a TDB2 dataset throws the following exception when issuing a query:
>
> {noformat}
> org.apache.jena.dboe.transaction.txn.TransactionException: Iterator used inside a different transaction
> at org.apache.jena.tdb2.store.IteratorTxnTracker.check(IteratorTxnTracker.java:53)
> at org.apache.jena.tdb2.store.IteratorTxnTracker.hasNext(IteratorTxnTracker.java:41)
> at org.apache.jena.atlas.iterator.Iter$2.hasNext(Iter.java:265)
> at org.apache.jena.atlas.iterator.Iter.hasNext(Iter.java:903)
> at org.apache.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
> at org.apache.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:105)
> at org.apache.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:105)
> at org.apache.jena.reasoner.rulesys.impl.TopLevelTripleMatchFrame.nextMatch(TopLevelTripleMatchFrame.java:55)
> at org.apache.jena.reasoner.rulesys.impl.LPInterpreter.run(LPInterpreter.java:328)
> at org.apache.jena.reasoner.rulesys.impl.LPInterpreter.next(LPInterpreter.java:190)
> at org.apache.jena.reasoner.rulesys.impl.Generator.pump(Generator.java:252)
> at org.apache.jena.reasoner.rulesys.impl.Generator.pump(Generator.java:239)
> at org.apache.jena.reasoner.rulesys.impl.LPBRuleEngine.pump(LPBRuleEngine.java:359)
> at org.apache.jena.reasoner.rulesys.impl.LPTopGoalIterator.moveForward(LPTopGoalIterator.java:107)
> at org.apache.jena.reasoner.rulesys.impl.LPTopGoalIterator.hasNext(LPTopGoalIterator.java:223)
> at org.apache.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
> at org.apache.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
> at org.apache.jena.util.iterator.FilterIterator.hasNext(FilterIterator.java:55)
> at org.apache.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
> at org.apache.jena.util.iterator.FilterIterator.hasNext(FilterIterator.java:55)
> at org.apache.jena.sparql.engine.iterator.QueryIterTriplePattern$TripleMapper.hasNextBinding(QueryIterTriplePattern.java:135)
> at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
> at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:74)
> at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
> at org.apache.jena.sparql.engine.iterator.QueryIterBlockTriples.hasNextBinding(QueryIterBlockTriples.java:63)
> at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
> at org.apache.jena.sparql.engine.iterator.QueryIterSlice.hasNextBinding(QueryIterSlice.java:76)
> at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
> at org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:39)
> at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
> at org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:39)
> at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
> at org.apache.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStream.java:74)
> at org.apache.jena.sparql.engine.ResultSetCheckCondition.hasNext(ResultSetCheckCondition.java:55)
> at org.apache.jena.sparql.resultset.ResultSetApply.apply(ResultSetApply.java:38)
> at org.apache.jena.riot.resultset.rw.ResultSetWriterJSON.write(ResultSetWriterJSON.java:82)
> at org.apache.jena.riot.resultset.rw.ResultsWriter.write(ResultsWriter.java:127)
> at org.apache.jena.riot.resultset.rw.ResultsWriter.write(ResultsWriter.java:97)
> at org.apache.jena.fuseki.servlets.ResponseResultSet.lambda$generalOutput$1(ResponseResultSet.java:209)
> at org.apache.jena.fuseki.servlets.ResponseResultSet.output(ResponseResultSet.java:225)
> at org.apache.jena.fuseki.servlets.ResponseResultSet.generalOutput(ResponseResultSet.java:215)
> at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet$(ResponseResultSet.java:176)
> at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet(ResponseResultSet.java:85)
> at org.apache.jena.fuseki.servlets.SPARQL_Query.sendResults(SPARQL_Query.java:404)
> at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:286)
> at org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:238)
> at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:213)
> at org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:243)
> at org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:134)
> at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:74)
> at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73)
> at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1642)
> at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
> at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
> at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
> at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
> at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
> at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)
> at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
> at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
> at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
> at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)
> at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
> at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
> at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1642)
> at org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285)
> at org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248)
> at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1634)
> at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146)
> at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
> at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
> at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257)
> at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
> at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255)
> at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1340)
> at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203)
> at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
> at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
> at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201)
> at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1242)
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144)
> at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:740)
> at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
> at org.eclipse.jetty.server.Server.handle(Server.java:503)
> at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:364)
> at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:260)
> at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:305)
> at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103)
> at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:118)
> at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:333)
> at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:310)
> at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:168)
> at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:132)
> at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:765)
> at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:683)
> at java.lang.Thread.run(Thread.java:748){noformat}
>
> Steps to reproduce (see attachments for files)
>
> 1. Generate a tdb2 database from the toy data
> {code:java}
> $tdb2.tdbloader --loc=graph data.nt{code}
> 2. Start fuseki-server with the attached config (adjust path to ontology file in the config accordingly)
> {code:java}
> $fuseki-server --config=example.ttl{code}
> 3. Issue a small query
> {code:java}
> $s-query --server=http://localhost:3030/example "select * where {?s a <http://example.com/ns/Person>} limit 10"{code}
> 4. Issue another query
> {code:java}
> $s-query --server=http://localhost:3030/example "select * where {?s a <http://example.com/ns/Person>} limit 1000"{code}
> At this point, I consistently get this response:
> {code:java}
> Error 500: Iterator used inside a different transaction
> 500: http://localhost:3030/example?query=select+%2A+where+%7B%3Fs+a+%3Chttp%3A%2F%2Fexample.com%2Fns%2FPerson%3E%7D+limit+1000{code}
> And on the server log see the above stack trace. I have encountered this in both the 3.11 and 3.10 releases. I have not tried on earlier versions.
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