Hi all, Does anyone have an idea how to achieve the situation described in my message below?
Regards, Barry -----Original Message----- From: Nouwt, B. (Barry) <[email protected]> Sent: vrijdag 12 juli 2019 15:24 To: [email protected] Subject: RE: TDBTransactionException: Not in a transaction Hi Andy, thanks for the update! Maybe there is another way to get the setup that I want without having JENA-1667 arise. This is the setup I want: - a single dataset with two named graphs (that I can access and update separately, but having separate storage locations is not a requirement. It could also be in memory) - the default graph of the dataset is a Secured Model that uses our custom permissions Evaluator - the Secured Model contains the union of the two named graphs. - configurable via an fuseki assembler .TTL file Any idea how to achieve this without bumping into JENA-1667? Regards, Barry -----Original Message----- From: Andy Seaborne <[email protected]> Sent: donderdag 11 juli 2019 18:34 To: [email protected] Subject: Re: TDBTransactionException: Not in a transaction Barry, Quick update - it's the mixed database sources in the union graph causing the problems (so it is JENA-1667). There is a partial fix possible (would work in your case) but there are related more complicated cases that won't work so simply to be looked at. Andy On 10/07/2019 10:26, Andy Seaborne wrote: > Barry - excellent. I've got it reproduced on my system now. > > Thanks > > Andy > > > On 09/07/2019 09:57, Nouwt, B. (Barry) wrote: >> Hi Andy/rest, >> >> I've created an Java example in which the Exception occurs in Jena >> version 3.12.0. It uses Maven for dependency resolution and the >> Exception happens when you run the Java class JenaExample. >> >> See: https://github.com/barrynl/jena-example >> >> Regards, Barry >> >> -----Original Message----- >> From: Andy Seaborne <[email protected]> >> Sent: maandag 8 juli 2019 16:53 >> To: [email protected] >> Subject: Re: TDBTransactionException: Not in a transaction >> >> Some things have improved since 3.9.0. >> >> Barry - can you turn this into a minimal, free standing example? It's >> not manifesting in the same way as JENA-1667. >> >> Thanks >> Andy >> >> On 08/07/2019 15:20, Nouwt, B. (Barry) wrote: >>> 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(DatasetG >>> raphTransaction.java:140) >>> >>> > at >>> org.apache.jena.tdb.transaction.DatasetGraphTransaction.get(DatasetG >>> raphTransaction.java:52) >>> >>> > at >>> org.apache.jena.sparql.core.DatasetGraphWrapper.getR(DatasetGraphWra >>> pper.java:78) >>> >>> > at >>> org.apache.jena.sparql.core.DatasetGraphWrapper.find(DatasetGraphWra >>> pper.java:167) >>> >>> > at >>> org.apache.jena.sparql.core.GraphView.graphBaseFind(GraphView.java:1 >>> 24) >>> > at >>> org.apache.jena.sparql.core.GraphView.graphBaseFind(GraphView.java:1 >>> 16) >>> > at >>> org.apache.jena.graph.impl.GraphBase.find(GraphBase.java:241) >>> > at >>> org.apache.jena.graph.compose.MultiUnion.multiGraphFind(MultiUnion.j >>> ava:170) >>> >>> > at >>> org.apache.jena.graph.compose.MultiUnion.graphBaseFind(MultiUnion.ja >>> va:147) >>> >>> > at >>> org.apache.jena.graph.impl.GraphBase.find(GraphBase.java:241) >>> > at >>> org.apache.jena.graph.impl.GraphBase.graphBaseFind(GraphBase.java:25 >>> 8) >>> > at >>> org.apache.jena.graph.impl.GraphBase.find(GraphBase.java:255) >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIterTriplePattern$Triple >>> Mapper.<init>(QueryIterTriplePattern.java:75) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIterTriplePattern.nextSt >>> age(QueryIterTriplePattern.java:49) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.makeNext >>> Stage(QueryIterRepeatApply.java:108) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextB >>> inding(QueryIterRepeatApply.java:65) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(Que >>> ryIteratorBase.java:114) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIterBlockTriples.hasNext >>> Binding(QueryIterBlockTriples.java:63) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(Que >>> ryIteratorBase.java:114) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIterConvert.hasNextBindi >>> ng(QueryIterConvert.java:58) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(Que >>> ryIteratorBase.java:114) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextB >>> inding(QueryIteratorWrapper.java:39) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(Que >>> ryIteratorBase.java:114) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextB >>> inding(QueryIteratorWrapper.java:39) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(Que >>> ryIteratorBase.java:114) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextB >>> inding(QueryIteratorWrapper.java:39) >>> >>> > at >>> org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(Que >>> ryIteratorBase.java:114) >>> >>> > at >>> org.apache.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStrea >>> m.java:74) >>> >>> > at >>> org.apache.jena.sparql.engine.ResultSetCheckCondition.hasNext(Result >>> SetCheckCondition.java:55) >>> >>> > at >>> org.apache.jena.fuseki.servlets.SPARQL_Query.executeQuery(SPARQL_Que >>> ry.java:350) >>> >>> > at >>> org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.ja >>> va:288) >>> >>> > at >>> org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SP >>> ARQL_Query.java:242) >>> >>> > at >>> org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.ja >>> va:227) >>> >>> > at >>> org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(Actio >>> nService.java:183) >>> >>> > at >>> org.apache.jena.fuseki.servlets.ActionService.execCommonWorker(Actio >>> nService.java:98) >>> >>> > at >>> org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java: >>> 74) >>> > at >>> org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.j >>> ava:73) >>> >>> > at >>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(Servle >>> tHandler.java:1642) >>> >>> > at >>> org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilt >>> erChain.java:61) >>> >>> > at >>> org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter. >>> java:108) >>> >>> > at >>> org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFil >>> ter.java:137) >>> >>> > at >>> org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRe >>> questFilter.java:125) >>> >>> > at >>> org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilt >>> erChain.java:66) >>> >>> > at >>> org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter. >>> java:108) >>> >>> > at >>> org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFil >>> ter.java:137) >>> >>> > at >>> org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRe >>> questFilter.java:125) >>> >>> > at >>> org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilt >>> erChain.java:66) >>> >>> > at >>> org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(Abstra >>> ctShiroFilter.java:449) >>> >>> > at >>> org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShir >>> oFilter.java:365) >>> >>> > at >>> org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCalla >>> ble.java:90) >>> >>> > at >>> org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallabl >>> e.java:83) >>> >>> > at >>> org.apache.shiro.subject.support.DelegatingSubject.execute(Delegatin >>> gSubject.java:383) >>> >>> > at >>> org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(Ab >>> stractShiroFilter.java:362) >>> >>> > at >>> org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRe >>> questFilter.java:125) >>> >>> > at >>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(Servle >>> tHandler.java:1642) >>> >>> > at >>> org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOrigin >>> Filter.java:285) >>> >>> > at >>> org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOrig >>> inFilter.java:248) >>> >>> > at >>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(Servle >>> tHandler.java:1634) >>> >>> > at >>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.jav >>> a:533) >>> >>> > at >>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler. >>> java:146) >>> >>> > at >>> org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.ja >>> va:548) >>> >>> > at >>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrappe >>> r.java:132) >>> >>> > at >>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHand >>> ler.java:257) >>> >>> > at >>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHand >>> ler.java:1595) >>> >>> > at >>> org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHand >>> ler.java:255) >>> >>> > at >>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHand >>> ler.java:1340) >>> >>> > at >>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandl >>> er.java:203) >>> >>> > at >>> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java >>> :473) >>> >>> > at >>> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandl >>> er.java:1564) >>> >>> > at >>> org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandl >>> er.java:201) >>> >>> > at >>> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandl >>> er.java:1242) >>> >>> > at >>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler. >>> java:144) >>> >>> > at >>> org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler >>> .java:690) >>> >>> > at >>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrappe >>> r.java:132) >>> >>> > at >>> org.eclipse.jetty.server.Server.handle(Server.java:503) >>> > at >>> org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:364) >>> > at >>> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.ja >>> va:260) >>> >>> > at >>> org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(Abstr >>> actConnection.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(QueuedThreadPo >>> ol.java:765) >>> >>> > at >>> org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPoo >>> l.java:683) >>> >>> > at java.lang.Thread.run(Thread.java:745) >>> > >>> > >>> > >>> > >>> > This message may contain information that is not intended >>> for you. If you are not the addressee or if this message was sent to >>> you by mistake, you are requested to inform the sender and delete >>> the message. TNO accepts no liability for the content of this >>> e-mail, for the manner in which you use it and for damage of any >>> kind resulting from the risks inherent to the electronic transmission of >>> messages. >>> > >>> -- >>> Lorenz Bühmann >>> AKSW group, University of Leipzig >>> Group: http://aksw.org - semantic web research center >>> >>> >>> >>> This message may contain information that is not intended for you. If you are not the addressee or if this message was sent to you by mistake, you are requested to inform the sender and delete the message. TNO accepts no liability for the content of this e-mail, for the manner in which you use it and for damage of any kind resulting from the risks inherent to the electronic transmission of messages.
