On 07/03/18 12:44, Mikael Pesonen wrote:
So can we make backup quads, empty database and insert quads back, and then we have a noncorrupted database?
It can't be guaranteed. If the quad dump is valid RDF, the new database will not be corrupted.But a dump of a broken database may be incomplete in some way. It is unusual but possible.
Andy
On 5.3.2018 16:41, ajs6f wrote:To my knowledge (Andy of course is the TDB expert) you can't really rebuild a TDB instance from a corrupted TDB instance. You should start with a known-good backup or original RDF files.ajs6fOn Mar 5, 2018, at 9:32 AM, Mikael Pesonen <mikael.peso...@lingsoft.fi> wrote:Still having these issues on all of our installations.I'm going to rule out corrupted database on our oldest server. What would be preferred way to rebuild data?Data folder: 5226102784 Mar 5 12:48 GOSP.dat 260046848 Mar 5 12:48 GOSP.idn 5377097728 Mar 5 12:48 GPOS.dat 268435456 Mar 5 12:48 GPOS.idn 5486149632 Mar 5 12:48 GSPO.dat 285212672 Mar 5 12:48 GSPO.idn 0 Mar 5 12:48 journal.jrnl 545259520 Mar 5 12:38 node2id.dat 150994944 Feb 20 16:32 node2id.idn 497658012 Mar 5 12:38 nodes.dat 1 Nov 14 15:27 none.opt 33554432 Jan 24 17:06 OSP.dat 4848615424 Mar 5 12:48 OSPG.dat 293601280 Mar 1 12:46 OSPG.idn 8388608 Jan 24 16:59 OSP.idn 25165824 Jan 24 17:06 POS.dat 4966055936 Mar 5 12:48 POSG.dat 276824064 Mar 5 12:38 POSG.idn 8388608 Jan 24 16:55 POS.idn 8388608 Jan 31 12:06 prefix2id.dat 8388608 Mar 15 2016 prefix2id.idn 6771 Jan 31 12:06 prefixes.dat 25165824 Jan 31 12:06 prefixIdx.dat 8388608 Jan 8 13:19 prefixIdx.idn 33554432 Jan 24 17:06 SPO.dat 5075107840 Mar 5 12:48 SPOG.dat 369098752 Mar 5 12:48 SPOG.idn 8388608 Jan 24 17:04 SPO.idn 4069 Nov 7 16:38 _stats.opt 4 Feb 6 12:01 tdb.lock On 30.1.2018 15:04, Andy Seaborne wrote:These seem to be different errors. "In the middle of an alloc-write" is possibly a concurrency issue. "Failed to read" is possibly a previous corrupted databaseThis is a text dataset? That should be using an MRSW lock to get some level isolation.What's the Fuseki config in this case? Andy On 24/01/18 23:40, Chris Tomlinson wrote:On the latest 3.7.0-Snapshot (master branch) I also saw repeated occurrences of this the other day while running some queries from the fuseki browser app and with a database load going on with our own app using:DatasetAccessorFactory.createHTTP(baseUrl+"/data”); with for the first model to transfer: DatasetAccessor putModel(graphName, m); and for following models:static void addToTransferBulk(final String graphName, final Model m) {if (currentDataset == null) currentDataset = DatasetFactory.createGeneral(); currentDataset.addNamedModel(graphName, m); triplesInDataset += m.size(); if (triplesInDataset > initialLoadBulkSize) { try { loadDatasetMutex(currentDataset); currentDataset = null; triplesInDataset = 0; } catch (TimeoutException e) { e.printStackTrace(); return; } } }as I say the exceptions appeared while I was running some queries from from the fuseki browser app:[2018-01-22 16:25:02] Fuseki INFO [475] 200 OK (17.050 s)[2018-01-22 16:25:03] Fuseki INFO [477] POST http://localhost:13180/fuseki/bdrcrw[2018-01-22 16:25:03] BindingTDB ERROR get1(?lit)org.apache.jena.tdb.base.file.FileException: In the middle of an alloc-write at org.apache.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:311) at org.apache.jena.tdb.base.objectfile.ObjectFileWrapper.read(ObjectFileWrapper.java:57)at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78)at org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:186) at org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:111) at org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:70) at org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128) at org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82) at org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50) at org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67) at org.apache.jena.tdb.solver.BindingTDB.get1(BindingTDB.java:122) at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121)at org.apache.jena.sparql.expr.ExprVar.eval(ExprVar.java:60) at org.apache.jena.sparql.expr.ExprVar.eval(ExprVar.java:53) at org.apache.jena.sparql.expr.ExprNode.eval(ExprNode.java:93)at org.apache.jena.sparql.expr.ExprFunction2.eval(ExprFunction2.java:76) at org.apache.jena.sparql.expr.E_LogicalOr.evalSpecial(E_LogicalOr.java:58) at org.apache.jena.sparql.expr.ExprFunction2.eval(ExprFunction2.java:72) at org.apache.jena.sparql.expr.ExprNode.isSatisfied(ExprNode.java:41) at org.apache.jena.sparql.engine.iterator.QueryIterFilterExpr.accept(QueryIterFilterExpr.java:49) at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:69) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:66) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:66) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterConcat.hasNextBinding(QueryIterConcat.java:82) 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.QueryIterConvert.hasNextBinding(QueryIterConvert.java:58) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.getInputNextUnseen(QueryIterDistinct.java:104) at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.hasNextBinding(QueryIterDistinct.java:70) 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.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:125) at org.apache.jena.riot.resultset.rw.ResultsWriter.write(ResultsWriter.java:95) at org.apache.jena.fuseki.servlets.ResponseResultSet.lambda$1(ResponseResultSet.java:210) at org.apache.jena.fuseki.servlets.ResponseResultSet.output(ResponseResultSet.java:226) at org.apache.jena.fuseki.servlets.ResponseResultSet.generalOutput(ResponseResultSet.java:216) at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet$(ResponseResultSet.java:177) at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet(ResponseResultSet.java:86) at org.apache.jena.fuseki.servlets.SPARQL_Query.sendResults(SPARQL_Query.java:389) at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:268) at org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:224) at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:199) at org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:192) at org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:106) at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:73) at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) 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$1.call(AbstractShiroFilter.java:365) at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285) at org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:94) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:504) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1104) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1519) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1475) 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) [2018-01-22 16:25:03] BindingTDB ERROR get1(?lit)org.apache.jena.tdb.base.file.FileException: In the middle of an alloc-write at org.apache.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:311) at org.apache.jena.tdb.base.objectfile.ObjectFileWrapper.read(ObjectFileWrapper.java:57)at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78)at org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:186) at org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:111) at org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:70) at org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128) at org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82) at org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50) at org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67) at org.apache.jena.tdb.solver.BindingTDB.get1(BindingTDB.java:122) at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121)at org.apache.jena.sparql.expr.ExprVar.eval(ExprVar.java:60) at org.apache.jena.sparql.expr.ExprVar.eval(ExprVar.java:53) at org.apache.jena.sparql.expr.ExprNode.eval(ExprNode.java:93)at org.apache.jena.sparql.expr.ExprFunction2.eval(ExprFunction2.java:76) at org.apache.jena.sparql.expr.E_LogicalOr.evalSpecial(E_LogicalOr.java:58) at org.apache.jena.sparql.expr.ExprFunction2.eval(ExprFunction2.java:72) at org.apache.jena.sparql.expr.ExprNode.isSatisfied(ExprNode.java:41) at org.apache.jena.sparql.engine.iterator.QueryIterFilterExpr.accept(QueryIterFilterExpr.java:49) at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:69) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:66) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:66) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterConcat.hasNextBinding(QueryIterConcat.java:82) 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.QueryIterConvert.hasNextBinding(QueryIterConvert.java:58) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.getInputNextUnseen(QueryIterDistinct.java:104) at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.hasNextBinding(QueryIterDistinct.java:70) 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.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:125) at org.apache.jena.riot.resultset.rw.ResultsWriter.write(ResultsWriter.java:95) at org.apache.jena.fuseki.servlets.ResponseResultSet.lambda$1(ResponseResultSet.java:210) at org.apache.jena.fuseki.servlets.ResponseResultSet.output(ResponseResultSet.java:226) at org.apache.jena.fuseki.servlets.ResponseResultSet.generalOutput(ResponseResultSet.java:216) at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet$(ResponseResultSet.java:177) at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet(ResponseResultSet.java:86) at org.apache.jena.fuseki.servlets.SPARQL_Query.sendResults(SPARQL_Query.java:389) at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:268) at org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:224) at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:199) at org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:192) at org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:106) at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:73) at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) 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$1.call(AbstractShiroFilter.java:365) at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285) at org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:94) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:504) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1104) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1519) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1475) 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) [2018-01-22 16:25:03] BindingTDB ERROR get1(?lit)org.apache.jena.tdb.base.file.FileException: In the middle of an alloc-write at org.apache.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:311) at org.apache.jena.tdb.base.objectfile.ObjectFileWrapper.read(ObjectFileWrapper.java:57)at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78)at org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:186) at org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:111) at org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:70) at org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128) at org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82) at org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50) at org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67) at org.apache.jena.tdb.solver.BindingTDB.get1(BindingTDB.java:122) at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121)at org.apache.jena.sparql.expr.ExprVar.eval(ExprVar.java:60) at org.apache.jena.sparql.expr.ExprVar.eval(ExprVar.java:53) at org.apache.jena.sparql.expr.ExprNode.eval(ExprNode.java:93)at org.apache.jena.sparql.expr.ExprFunction2.eval(ExprFunction2.java:76) at org.apache.jena.sparql.expr.E_LogicalOr.evalSpecial(E_LogicalOr.java:58) at org.apache.jena.sparql.expr.ExprFunction2.eval(ExprFunction2.java:72) at org.apache.jena.sparql.expr.ExprNode.isSatisfied(ExprNode.java:41) at org.apache.jena.sparql.engine.iterator.QueryIterFilterExpr.accept(QueryIterFilterExpr.java:49) at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:69) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:66) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:66) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterConcat.hasNextBinding(QueryIterConcat.java:82) 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.QueryIterConvert.hasNextBinding(QueryIterConvert.java:58) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.getInputNextUnseen(QueryIterDistinct.java:104) at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.hasNextBinding(QueryIterDistinct.java:70) 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.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:125) at org.apache.jena.riot.resultset.rw.ResultsWriter.write(ResultsWriter.java:95) at org.apache.jena.fuseki.servlets.ResponseResultSet.lambda$1(ResponseResultSet.java:210) at org.apache.jena.fuseki.servlets.ResponseResultSet.output(ResponseResultSet.java:226) at org.apache.jena.fuseki.servlets.ResponseResultSet.generalOutput(ResponseResultSet.java:216) at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet$(ResponseResultSet.java:177) at org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet(ResponseResultSet.java:86) at org.apache.jena.fuseki.servlets.SPARQL_Query.sendResults(SPARQL_Query.java:389) at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:268) at org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:224) at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:199) at org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:192) at org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:106) at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:73) at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) 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$1.call(AbstractShiroFilter.java:365) at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:285) at org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:248) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:94) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:504) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1104) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1519) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1475) 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)On Jan 24, 2018, at 10:31 AM, Mikael Pesonen <mikael.peso...@lingsoft.fi> wrote:And running the test set with 1 concurrent loop, it was repeated 10000 times without errors. So error occurs only with more than one concurrent operations.On 24.1.2018 17:40, ajs6f wrote:Please show your code, including Fuseki config. It's hard to diagnose what is going wrong when we don't know what is supposed to happen.ajs6fOn Jan 24, 2018, at 10:26 AM, Mikael Pesonen <mikael.peso...@lingsoft.fi> wrote:Hi,I have a test script running 10 concurrent CRUD operations in a loop. After few operations I get HTTP error 500 and these are in fuseki server output. Am I doing something wrong here?[2018-01-24 17:16:53] BindingTDB ERROR get1(?o)org.apache.jena.tdb.base.file.FileException: ObjectFileStorage.read[nodes](491421708)[filesize=495059272][file.size()=495059272]: Failed to read the length : got 0 bytes at org.apache.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:341) at org.apache.jena.tdb.base.objectfile.ObjectFileWrapper.read(ObjectFileWrapper.java:57) at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78) at org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:186) at org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:111) at org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:70) at org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128) at org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82) at org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50) at org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67) at org.apache.jena.tdb.solver.BindingTDB.get1(BindingTDB.java:122) at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121) at org.apache.jena.sparql.engine.binding.BindingFactory.materialize(BindingFactory.java:60) at org.apache.jena.tdb.solver.QueryEngineTDB$QueryIteratorMaterializeBinding.moveToNextBinding(QueryEngineTDB.java:131) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.nextBinding(QueryIteratorBase.java:156) at org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.moveToNextBinding(QueryIteratorWrapper.java:42) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.nextBinding(QueryIteratorBase.java:156) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.next(QueryIteratorBase.java:131) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.next(QueryIteratorBase.java:40)at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:270)at org.apache.jena.ext.com.google.common.collect.MultitransformedIterator.hasNext(MultitransformedIterator.java:52) at org.apache.jena.ext.com.google.common.collect.MultitransformedIterator.hasNext(MultitransformedIterator.java:50)at java.util.Iterator.forEachRemaining(Iterator.java:115)at org.apache.jena.sparql.engine.QueryExecutionBase.execConstructDataset(QueryExecutionBase.java:243) at org.apache.jena.sparql.engine.QueryExecutionBase.execConstructDataset(QueryExecutionBase.java:236) at org.apache.jena.fuseki.servlets.SPARQL_Query.executeQuery(SPARQL_Query.java:331) at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:270) at org.apache.jena.fuseki.servlets.SPARQL_Query.executeBody(SPARQL_Query.java:239) at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:219) at org.apache.jena.fuseki.servlets.ActionSPARQL.executeLifecycle(ActionSPARQL.java:132) at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeRequest(SPARQL_UberServlet.java:356) at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeAction(SPARQL_UberServlet.java:220) at org.apache.jena.fuseki.servlets.ActionSPARQL.execCommonWorker(ActionSPARQL.java:83) at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:82) at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637) 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:1637) 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$CachedChain.doFilter(ServletHandler.java:1629) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:455) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)at org.eclipse.jetty.server.Server.handle(Server.java:561)at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:334) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:104) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:243) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:679) at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:597)at java.lang.Thread.run(Thread.java:745) [2018-01-24 17:16:53] Fuseki INFO [644] 204 No Content (2 ms)[2018-01-24 17:16:53] BindingHashMap WARN Binding.add: null value - ignored[2018-01-24 17:16:57] BindingTDB ERROR get1(?p)org.apache.jena.tdb.base.file.FileException: In the middle of an alloc-write at org.apache.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:311) at org.apache.jena.tdb.base.objectfile.ObjectFileWrapper.read(ObjectFileWrapper.java:57) at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78) at org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:186) at org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:111) at org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:70) at org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128) at org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82) at org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50) at org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67) at org.apache.jena.tdb.solver.BindingTDB.get1(BindingTDB.java:122) at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121) at org.apache.jena.sparql.engine.binding.BindingFactory.materialize(BindingFactory.java:60) at org.apache.jena.tdb.solver.QueryEngineTDB$QueryIteratorMaterializeBinding.moveToNextBinding(QueryEngineTDB.java:131) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.nextBinding(QueryIteratorBase.java:156) at org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.moveToNextBinding(QueryIteratorWrapper.java:42) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.nextBinding(QueryIteratorBase.java:156) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.next(QueryIteratorBase.java:131) at org.apache.jena.sparql.engine.iterator.QueryIteratorBase.next(QueryIteratorBase.java:40)at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:270)at org.apache.jena.ext.com.google.common.collect.MultitransformedIterator.hasNext(MultitransformedIterator.java:52) at org.apache.jena.ext.com.google.common.collect.MultitransformedIterator.hasNext(MultitransformedIterator.java:50)at java.util.Iterator.forEachRemaining(Iterator.java:115)at org.apache.jena.sparql.engine.QueryExecutionBase.execConstructDataset(QueryExecutionBase.java:243) at org.apache.jena.sparql.engine.QueryExecutionBase.execConstructDataset(QueryExecutionBase.java:236) at org.apache.jena.fuseki.servlets.SPARQL_Query.executeQuery(SPARQL_Query.java:331) at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:270) at org.apache.jena.fuseki.servlets.SPARQL_Query.executeBody(SPARQL_Query.java:239) at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:219) at org.apache.jena.fuseki.servlets.ActionSPARQL.executeLifecycle(ActionSPARQL.java:132) at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeRequest(SPARQL_UberServlet.java:356) at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeAction(SPARQL_UberServlet.java:220) at org.apache.jena.fuseki.servlets.ActionSPARQL.execCommonWorker(ActionSPARQL.java:83) at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:82) at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637) 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:1637) 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$CachedChain.doFilter(ServletHandler.java:1629) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:455) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)at org.eclipse.jetty.server.Server.handle(Server.java:561)at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:334) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:104) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:243) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:679) at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:597)at java.lang.Thread.run(Thread.java:745)[2018-01-24 17:16:57] Fuseki INFO [1027] 204 No Content (13 ms) [2018-01-24 17:16:57] BindingHashMap WARN Binding.add: null value - ignored[2018-01-24 17:17:02] BindingTDB ERROR get1(?s)org.apache.jena.tdb.base.file.FileException: In the middle of an alloc-write at org.apache.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:311) at org.apache.jena.tdb.base.objectfile.ObjectFileWrapper.read(ObjectFileWrapper.java:57) at org.apache.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78) at org.apache.jena.tdb.store.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:186) at org.apache.jena.tdb.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:111) at org.apache.jena.tdb.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:70) at org.apache.jena.tdb.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:128) at org.apache.jena.tdb.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:82) at org.apache.jena.tdb.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:50) at org.apache.jena.tdb.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67) at org.apache.jena.tdb.solver.BindingTDB.get1(BindingTDB.java:122) at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121) at org.apache.jena.sparql.engine.binding.BindingProjectBase.get1(BindingProjectBase.java:52) at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121) at org.apache.jena.sparql.engine.binding.BindingProjectBase.get1(BindingProjectBase.java:52) at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:121) at org.apache.jena.sparql.engine.binding.BindingBase.hashCode(BindingBase.java:201) at org.apache.jena.sparql.engine.binding.BindingBase.hashCode(BindingBase.java:183)at java.util.HashMap.hash(HashMap.java:338) at java.util.HashMap.containsKey(HashMap.java:595) at java.util.HashSet.contains(HashSet.java:203)at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.getInputNextUnseen(QueryIterDistinct.java:106) at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.hasNextBinding(QueryIterDistinct.java:70) 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.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.fuseki.servlets.SPARQL_Query.executeQuery(SPARQL_Query.java:320) at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:270) at org.apache.jena.fuseki.servlets.SPARQL_Query.executeBody(SPARQL_Query.java:239) at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:219) at org.apache.jena.fuseki.servlets.ActionSPARQL.executeLifecycle(ActionSPARQL.java:132) at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeRequest(SPARQL_UberServlet.java:356) at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeAction(SPARQL_UberServlet.java:220) at org.apache.jena.fuseki.servlets.ActionSPARQL.execCommonWorker(ActionSPARQL.java:83) at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:82) at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637) 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:1637) 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$CachedChain.doFilter(ServletHandler.java:1629) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:455) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)at org.eclipse.jetty.server.Server.handle(Server.java:561)at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:334) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:104) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:243) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:679) at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:597)at java.lang.Thread.run(Thread.java:745) [2018-01-24 17:17:02] Fuseki WARN [1758] RC = 500 : null java.lang.NullPointerExceptionat org.apache.jena.sparql.engine.binding.BindingBase.hashCode(BindingBase.java:203) at org.apache.jena.sparql.engine.binding.BindingBase.hashCode(BindingBase.java:183)at java.util.HashMap.hash(HashMap.java:338) at java.util.HashMap.containsKey(HashMap.java:595) at java.util.HashSet.contains(HashSet.java:203)at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.getInputNextUnseen(QueryIterDistinct.java:106) at org.apache.jena.sparql.engine.iterator.QueryIterDistinct.hasNextBinding(QueryIterDistinct.java:70) 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.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.fuseki.servlets.SPARQL_Query.executeQuery(SPARQL_Query.java:320) at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:270) at org.apache.jena.fuseki.servlets.SPARQL_Query.executeBody(SPARQL_Query.java:239) at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:219) at org.apache.jena.fuseki.servlets.ActionSPARQL.executeLifecycle(ActionSPARQL.java:132) at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeRequest(SPARQL_UberServlet.java:356) at org.apache.jena.fuseki.servlets.SPARQL_UberServlet.executeAction(SPARQL_UberServlet.java:220) at org.apache.jena.fuseki.servlets.ActionSPARQL.execCommonWorker(ActionSPARQL.java:83) at org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:82) at org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637) 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:1637) 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$CachedChain.doFilter(ServletHandler.java:1629) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:455) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)at org.eclipse.jetty.server.Server.handle(Server.java:561)at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:334) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:104) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:243) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:679) at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:597)at java.lang.Thread.run(Thread.java:745)[2018-01-24 17:17:02] Fuseki INFO [1759] 204 No Content (11 ms) [2018-01-24 17:17:02] Fuseki INFO [1758] 500 Server Error (11 ms)-- Lingsoft - 30 years of Leading Language Management www.lingsoft.fiSpeech Applications - Language Management - Translation - Reader's and Writer's Tools - Text Tools - E-books and M-booksMikael Pesonen System Engineer e-mail: mikael.peso...@lingsoft.fi Tel. +358 2 279 3300 Time zone: GMT+2 Helsinki Office Eteläranta 10 FI-00130 Helsinki FINLAND Turku Office Kauppiaskatu 5 A FI-20100 Turku FINLAND-- Lingsoft - 30 years of Leading Language Management www.lingsoft.fiSpeech Applications - Language Management - Translation - Reader's and Writer's Tools - Text Tools - E-books and M-booksMikael Pesonen System Engineer e-mail: mikael.peso...@lingsoft.fi Tel. +358 2 279 3300 Time zone: GMT+2 Helsinki Office Eteläranta 10 FI-00130 Helsinki FINLAND Turku Office Kauppiaskatu 5 A FI-20100 Turku FINLAND-- Lingsoft - 30 years of Leading Language Management www.lingsoft.fiSpeech Applications - Language Management - Translation - Reader's and Writer's Tools - Text Tools - E-books and M-booksMikael Pesonen System Engineer e-mail: mikael.peso...@lingsoft.fi Tel. +358 2 279 3300 Time zone: GMT+2 Helsinki Office Eteläranta 10 FI-00130 Helsinki FINLAND Turku Office Kauppiaskatu 5 A FI-20100 Turku FINLAND