version?
On 02/08/18 10:06, Mikael Pesonen wrote:
It does happen in our test environment on high load quite often. More
sleep I put in the test script, less frequently error happens.
Most of the time transactions are executed after the error, but not
always. Fuseki never returns error. Rarely below error happens, don't
know if it's related.
I'm not able to produce a sendable script that would case these errors.
So as a fix I'm planning just to add enough sleep between every Fuseki
call. 50-100ms seems to work.
org.apache.jena.query.QueryException: Secondary index duplicate:
GSPO->GPOS -> [[0000000000A9D430], [0000000015AFB422],
[0000000000002602], [04007E280A6A5DC0]]
at
org.apache.jena.sparql.lang.ParserARQUpdate._parse(ParserARQUpdate.java:78)
at
org.apache.jena.sparql.lang.ParserARQUpdate.parse$(ParserARQUpdate.java:45)
at
org.apache.jena.sparql.lang.UpdateParser.parse(UpdateParser.java:48)
at
org.apache.jena.update.UpdateAction.parseExecute(UpdateAction.java:421)
at
org.apache.jena.update.UpdateAction.parseExecute(UpdateAction.java:380)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:234)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.executeBody(SPARQL_Update.java:189)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:106)
at
org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:192)
at
org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:106)
at
org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:73)
at
org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:73)
at
org.eclipse.jetty.servlet.ServletHandler$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$2.run(QueuedThreadPool.java:597)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.jena.tdb.TDBException: Secondary index duplicate:
GSPO->GPOS -> [[0000000000A9D430], [0000000015AFB422],
[0000000000002602], [04007E280A6A5DC0]]
at
org.apache.jena.tdb.store.tupletable.TupleTable.add(TupleTable.java:103)
at
org.apache.jena.tdb.store.nodetupletable.NodeTupleTableConcrete.addRow(NodeTupleTableConcrete.java:88)
at org.apache.jena.tdb.store.QuadTable.add(QuadTable.java:60)
at
org.apache.jena.tdb.store.DatasetGraphTDB.addToNamedGraph(DatasetGraphTDB.java:97)
at
org.apache.jena.sparql.core.DatasetGraphTriplesQuads.add(DatasetGraphTriplesQuads.java:44)
at
org.apache.jena.sparql.core.DatasetGraphTriplesQuads.add(DatasetGraphTriplesQuads.java:31)
at
org.apache.jena.sparql.core.DatasetGraphWrapper.add(DatasetGraphWrapper.java:116)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.addToDatasetGraph(UpdateEngineWorker.java:539)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.lambda$execInsert$4(UpdateEngineWorker.java:532)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.execInsert(UpdateEngineWorker.java:532)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.execInsert(UpdateEngineWorker.java:521)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.visit(UpdateEngineWorker.java:418)
at
org.apache.jena.sparql.modify.request.UpdateModify.visit(UpdateModify.java:100)
at
org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:46)
at
org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:26)
at
org.apache.jena.sparql.modify.UsingUpdateSink.send(UsingUpdateSink.java:61)
at
org.apache.jena.sparql.modify.UsingUpdateSink.send(UsingUpdateSink.java:31)
at
org.apache.jena.sparql.lang.SPARQLParserBase.emitUpdate(SPARQLParserBase.java:189)
at
org.apache.jena.sparql.lang.arq.ARQParser.Update1(ARQParser.java:1491)
at
org.apache.jena.sparql.lang.arq.ARQParser.Update(ARQParser.java:1419)
at
org.apache.jena.sparql.lang.arq.ARQParser.UpdateUnit(ARQParser.java:52)
at
org.apache.jena.sparql.lang.ParserARQUpdate._parse(ParserARQUpdate.java:62)
... 57 more
org.apache.jena.query.QueryException: Secondary index duplicate:
GSPO->GPOS -> [[0000000000A9D430], [0000000015AFB422],
[0000000000002602], [04007E280A6A5DC0]]
at
org.apache.jena.sparql.lang.ParserARQUpdate._parse(ParserARQUpdate.java:78)
at
org.apache.jena.sparql.lang.ParserARQUpdate.parse$(ParserARQUpdate.java:45)
at
org.apache.jena.sparql.lang.UpdateParser.parse(UpdateParser.java:48)
at
org.apache.jena.update.UpdateAction.parseExecute(UpdateAction.java:421)
at
org.apache.jena.update.UpdateAction.parseExecute(UpdateAction.java:380)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:234)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.executeBody(SPARQL_Update.java:189)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:106)
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.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$2.run(QueuedThreadPool.java:597)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.jena.tdb.TDBException: Secondary index duplicate:
GSPO->GPOS -> [[0000000000A9D430], [0000000015AFB422],
[0000000000002602], [04007E280A6A5DC0]]
at
org.apache.jena.tdb.store.tupletable.TupleTable.add(TupleTable.java:103)
at
org.apache.jena.tdb.store.nodetupletable.NodeTupleTableConcrete.addRow(NodeTupleTableConcrete.java:88)
at org.apache.jena.tdb.store.QuadTable.add(QuadTable.java:60)
at
org.apache.jena.tdb.store.DatasetGraphTDB.addToNamedGraph(DatasetGraphTDB.java:97)
at
org.apache.jena.sparql.core.DatasetGraphTriplesQuads.add(DatasetGraphTriplesQuads.java:44)
at
org.apache.jena.sparql.core.DatasetGraphTriplesQuads.add(DatasetGraphTriplesQuads.java:31)
at
org.apache.jena.sparql.core.DatasetGraphWrapper.add(DatasetGraphWrapper.java:116)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.addToDatasetGraph(UpdateEngineWorker.java:539)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.lambda$execInsert$4(UpdateEngineWorker.java:532)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.execInsert(UpdateEngineWorker.java:532)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.execInsert(UpdateEngineWorker.java:521)
at
org.apache.jena.sparql.modify.UpdateEngineWorker.visit(UpdateEngineWorker.java:418)
at
org.apache.jena.sparql.modify.request.UpdateModify.visit(UpdateModify.java:100)
at
org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:46)
at
org.apache.jena.sparql.modify.UpdateVisitorSink.send(UpdateVisitorSink.java:26)
at
org.apache.jena.sparql.modify.UsingUpdateSink.send(UsingUpdateSink.java:61)
at
org.apache.jena.sparql.modify.UsingUpdateSink.send(UsingUpdateSink.java:31)
at
org.apache.jena.sparql.lang.SPARQLParserBase.emitUpdate(SPARQLParserBase.java:189)
at
org.apache.jena.sparql.lang.arq.ARQParser.Update1(ARQParser.java:1491)
at
org.apache.jena.sparql.lang.arq.ARQParser.Update(ARQParser.java:1419)
at
org.apache.jena.sparql.lang.arq.ARQParser.UpdateUnit(ARQParser.java:52)
at
org.apache.jena.sparql.lang.ParserARQUpdate._parse(ParserARQUpdate.java:62)
... 57 more
On 2.8.2018 11:03, Andy Seaborne wrote:
(subject line changed - this is not the original thread report)
On 01/08/18 10:32, Mikael Pesonen wrote:
Hi,
is it somehow possible to get this error (TransactionManager ERROR
There are now active transactions ) from Fuseki GSP so that client
could sleep and retry later allowing db to finish the transaction?
No - it's an internal consistency check.
Does the transaction still happen?
Do you have a reproducible script to make this happen? I've never seen
it occur.
Andy
On 19.6.2018 23:56, Andy Seaborne wrote:
On 18/06/18 11:36, Mikael Pesonen wrote:
On 18.6.2018 13:30, Andy Seaborne wrote:
On 18/06/18 10:55, Mikael Pesonen wrote:
Hi Andy,
On 18.6.2018 12:05, Andy Seaborne wrote:
>>> errors occur less than before.
which errors?
TransactionManager ERROR There are now active transactions
This occurs when Im inserting new data and trying to read it right
away (get empty result), or deleting data and trying to read it to
make sure it's deleted (get data that should be deleted). There are
no other errors in the log.
From looking at the code, I can't see how that happens - is it now
possible to provide a reproducible script so that I can run it on
machine?
Andy
-ku
FINLAND
