Hi, thanks for the replies! @Lorenz: It would indeed be better to migrate to the latest version. Unfortunately, this would make the process a bit more complex...because the functionality I'm trying to add to Fuseki definitely works with version 3.9.0. Although you are right that the problem could be solved in a newer version...
@Rob: thanks for the pointer to that bug. At least I can keep my eye on that one, to see when it gets fixed. Regards, Barry -----Original Message----- From: Rob Vesse <[email protected]> Sent: maandag 8 juli 2019 14:55 To: [email protected] Subject: Re: TDBTransactionException: Not in a transaction This looks like a simpler variation upon JENA-1667 [1] which is a Known Bug that is not currently resolved in any version of Jena Although not sure why this worked in past versions of Fuseki, may be a side effect of other Fuseki refactoring that has happened Rob [1] https://issues.apache.org/jira/browse/JENA-1667 On 08/07/2019, 13:23, "Lorenz B." <[email protected]> wrote: Not that I could help here that much, but is there a reason for migrating from a and old version (2017-12) to a less old version (2018-09)? I mean, latest release is 3.12.0. Maybe this might already fix your problem? > Hi all, > > I am migrating my Apache Jena Fuseki from version 3.6.0 to version 3.9.0. However, the following configuration file gives a "TDBTransactionException: Not in a transaction" error when I send a SELECT query to its SPARQL endpoint. It worked as expected with Apache Jena Fuseki version 3.6.0. > > I've tried the following, but these things did not solve it: > > * Adding a tdb:DatasetTDB > * Use the same tdb:location for both GraphTDB's > > ----------------------------------------------- begin of config --------------------------------------------- > > # Licensed under the terms of http://www.apache.org/licenses/LICENSE-2.0 > > @prefix : <#> . > @prefix fuseki: <http://jena.apache.org/fuseki#> . > @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . > @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . > @prefix tdb: <http://jena.hpl.hp.com/2008/tdb#> . > @prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> . > @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . > > [] rdf:type fuseki:Server ; > fuseki:services ( > <#service1> > ) . > > # Custom code. > [] ja:loadClass "com.hp.hpl.jena.tdb.TDB" . > > # TDB > tdb:DatasetTDB rdfs:subClassOf ja:RDFDataset . > tdb:GraphTDB rdfs:subClassOf ja:Model . > > ## --------------------------------------------------------------- > ## Service with only SPARQL query on an inference model. > ## Inference model base data in TDB. > > <#service1> rdf:type fuseki:Service ; > fuseki:name "knowledge" ; > fuseki:serviceQuery "query" ; # SPARQL query service > fuseki:serviceUpdate "update" ; > fuseki:serviceUpload "upload" ; # Non-SPARQL upload service > fuseki:serviceReadWriteGraphStore "data" ; # SPARQL Graph store protocol (read and write) > # A separate read-only graph store endpoint: > fuseki:serviceReadGraphStore "get" ; # SPARQL Graph store protocol (read only) > fuseki:dataset <#dataset> . > > <#dataset> rdf:type ja:RDFDataset ; > ja:defaultGraph <#unionModel> ; > #set the timeout for a SPARQL query in milliseconds. 0 means no timeout and the query never times out. > ja:context [ ja:cxtName "arq:queryTimeout" ; ja:cxtValue "120000,240000" ] ; > ja:namedGraph [ > ja:graphName <https://www.tno.nl/agrifood/graph/pizza/onto> ; > ja:graph <#ontoGraph> ; > ]; > ja:namedGraph [ > ja:graphName <https://www.tno.nl/agrifood/graph/pizza/data> ; > ja:graph <#itemGraph> ; > ]. > > <#unionModel> rdf:type ja:UnionModel ; > ja:rootModel <#itemGraph> ; > ja:subModel <#ontoGraph> . > > <#ontoGraph> rdf:type tdb:GraphTDB ; > tdb:location "ontoDB" ; > tdb:graphName <https://www.tno.nl/agrifood/graph/pizza/onto> . > > <#itemGraph> rdf:type tdb:GraphTDB ; > tdb:location "itemDB" ; > tdb:graphName <https://www.tno.nl/agrifood/graph/pizza/data> . > > ------------------------------------------------------- end of config ------------------------------------------------- > > Any ideas how to fix the TDBTransactionException? (full trace below) > > Regards, Barry > > > org.apache.jena.tdb.transaction.TDBTransactionException: Not in a transaction > at org.apache.jena.tdb.transaction.DatasetGraphTransaction.get(DatasetGraphTransaction.java:140) > at org.apache.jena.tdb.transaction.DatasetGraphTransaction.get(DatasetGraphTransaction.java:52) > at org.apache.jena.sparql.core.DatasetGraphWrapper.getR(DatasetGraphWrapper.java:78) > at org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWrapper.java:167) > at org.apache.jena.sparql.core.GraphView.graphBaseFind(GraphView.java:124) > at org.apache.jena.sparql.core.GraphView.graphBaseFind(GraphView.java:116) > at org.apache.jena.graph.impl.GraphBase.find(GraphBase.java:241) > at org.apache.jena.graph.compose.MultiUnion.multiGraphFind(MultiUnion.java:170) > at org.apache.jena.graph.compose.MultiUnion.graphBaseFind(MultiUnion.java:147) > at org.apache.jena.graph.impl.GraphBase.find(GraphBase.java:241) > at org.apache.jena.graph.impl.GraphBase.graphBaseFind(GraphBase.java:258) > at org.apache.jena.graph.impl.GraphBase.find(GraphBase.java:255) > at org.apache.jena.sparql.engine.iterator.QueryIterTriplePattern$TripleMapper.<init>(QueryIterTriplePattern.java:75) > at org.apache.jena.sparql.engine.iterator.QueryIterTriplePattern.nextStage(QueryIterTriplePattern.java:49) > at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:108) > at org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) > 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.QueryIterConvert.hasNextBinding(QueryIterConvert.java:58) > 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:350) > at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:288) > at org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:242) > at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:227) > at org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:183) > at org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(ActionService.java:98) > 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.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$CachedChain.doFilter(ServletHandler.java:1634) > at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533) > at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146) > at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) > at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) > at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257) > at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595) > at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255) > at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1340) > at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203) > at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473) > at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564) > at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201) > at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1242) > at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144) > at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:690) > at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) > at org.eclipse.jetty.server.Server.handle(Server.java:503) > at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:364) > at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:260) > at org.eclipse.jetty.io.AbstractConnection$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.QueuedThreadPool.runJob(QueuedThreadPool.java:765) > at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:683) > at java.lang.Thread.run(Thread.java:745) > > > > > This message may contain information that is not intended for you. 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