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 <rve...@dotnetrdf.org>
Sent: maandag 8 juli 2019 14:55
To: users@jena.apache.org
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." <buehm...@informatik.uni-leipzig.de> 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)
>
>
>
>
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--
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center
