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ASF subversion and git services commented on JENA-1719: ------------------------------------------------------- Commit ddbaeaa0653fa0b60da500b8d14cfa6ea8cefe02 in jena's branch refs/heads/JENA-1719 from der [ https://gitbox.apache.org/repos/asf?p=jena.git;h=ddbaeaa ] JENA-1719: Work around for iterators being held across transactions > 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 > Priority: Major > Attachments: data.nt, example.owl, example.ttl > > > 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. -- This message was sent by Atlassian JIRA (v7.6.3#76005)