Having them in the same storage or one in memory would help.
This is the crux difficult in JENA-1667. How to know if a transaction
has already been started on a dataset when there are several levels of
models over the top.
At the moment, a union graph starts a transaction on its base graph, and
does nothing special about the others (that makes common cases work like
the Ont API and inference where other graph are either memory or same
storage).
Andy
On 12/07/2019 14:23, Nouwt, B. (Barry) wrote:
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 <a...@apache.org>
Sent: donderdag 11 juli 2019 18:34
To: users@jena.apache.org
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 <a...@apache.org>
Sent: maandag 8 juli 2019 16:53
To: users@jena.apache.org
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 <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(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
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