Hello,
I am trying to:
Set up Fuseki2 with inference and a TDB2 dataset in which can be
persisted named graphs created with SPARQL Update.
This is in order to:
- maintain a set of ontologies in a named graph
- maintain datasets in a number of named graphs
- perform reasoning in the union graphs
The assumption is that all data is persisted in a given TDB2 database.
The higher purpose is to use reasoning over ontologies when querying
over instance data located in named graphs. I think this is
conceptually what is discussed here:
Subject Re: Ontologies and model data
Date Mon, 03 Jun 2013 20:26:18 GMT
http://mail-archives.apache.org/mod_mbox/jena-users/201306.mbox/%3c51acfbea.2010...@apache.org%3E
The set up above is what comes across as a way of achieving this
higher goal but I am not sure either that it is the best set up.
Everything I have tried to do allows me to either perform inferences
in <urn:x-arq:UnionGraph> or to persist triples in named graphs in a
TDB2 database, but not both.
My problem is:
I cannot find a correct configuration that allows me to persist named
graphs added to a TDB2 dataset and have inference at the same time.
Some attempts are documented below.
I have done most of my test in apache-jena-fuseki-3.8.0, my last tries
were in apache-jena-fuseki-3.10.0.
Would somebody be in a position to advise or provide a minimal working
example?
With many thanks and best regards,
Pierre
###
Attempt 1:
# Example of a data service with SPARQL query abnd update on an
# inference model. Data is taken from TDB.
https://github.com/apache/jena/blob/master/jena-fuseki2/examples/service-inference-2.ttl
which I have adapted to use TDB2 (which basically meant updating the
namespace and the references to classes).
Outcome: This allows me to load data into named graphs and to perform
inferemce. However, it does not persist upon restarting the server.
###
Attempt 2:
Define two services pointing to different graphs as advised in
Subject Re: Persisting named graphs in TDB with jena-fuseki
Date Thu, 10 Mar 2016 14:47:10 GMT
http://mail-archives.apache.org/mod_mbox/jena-users/201603.mbox/%3cd30738c0.64a6f%25rve...@dotnetrdf.org%3E
Outcome: I could only manage de3fining two independent services on two
independent datasets and couldn't figure out how to link the TDB2 and
the Inference graphs.
A reference to https://issues.apache.org/jira/browse/JENA-1122
is made in
http://mail-archives.apache.org/mod_mbox/jena-users/201603.mbox/%3c56ec23e3.9010...@apache.org%3E
But I do not understand what is said here.
###
Attempt 3:
I have found a config that seemed t make the link that was needed
between graphs in Attempt 2 in:
https://stackoverflow.com/questions/47568703/named-graphs-v-default-graph-behaviour-in-apache-jena-fuseki
which I have adapted to TDB2.
However, this gives me:
ERROR Exception in initialization: caught: Not in tramsaction
This also seems to have been a cut off point in the thread mentioned
above
Subject Re: Configuring fuseki with TDB2 and OWL reasoning
Date Tue, 20 Feb 2018 10:55:13 GMT
http://mail-archives.apache.org/mod_mbox/jena-users/201802.mbox/%3C6d37a8c7-aca1-4c1c-0cd3-fa041ecc07eb%40apache.org%3E
This message refers to https://issues.apache.org/jira/browse/JENA-1492
which I do not understand but that comes across as having been
resolved. Indeed, I tested the config attached to it (probably as
minimal example for that issue) and it worked, but I don't think this
is the config I need.
#### ATTEMPT 3 Config
@prefix : <http://base/#> .
@prefix tdb2: <http://jena.apache.org/2016/tdb#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix fuseki: <http://jena.apache.org/fuseki#> .
# TDB2
#tdb2:DatasetTDB2 rdfs:subClassOf ja:RDFDataset .
#tdb2:GraphTDB rdfs:subClassOf ja:Model .
# Service 1: Dataset endpoint (no reasoning)
:dataService a fuseki:Service ;
fuseki:name "tdbEnpoint" ;
fuseki:serviceQuery "sparql", "query" ;
fuseki:serviceUpdate "update" ;
fuseki:dataset :tdbDataset ;
.
# Service 2: Reasoning endpoint
:reasoningService a fuseki:Service ;
fuseki:dataset :infDataset ;
fuseki:name "reasoningEndpoint" ;
fuseki:serviceQuery "query", "sparql" ;
fuseki:serviceReadGraphStore "get" ;
.
# Inference dataset
:infDataset rdf:type ja:RDFDataset ;
ja:defaultGraph :infModel ;
.
# Inference model
:infModel a ja:InfModel ;
ja:baseModel :g ;
ja:reasoner [
ja:reasonerURL
<http://jena.hpl.hp.com/2003/OWLFBRuleReasoner> ;
] ;
.
# Intermediate graph referencing the default union graph
:g rdf:type tdb2:GraphTDB ;
tdb2:dataset :tdbDataset ;
tdb2:graphName <urn:x-arq:UnionGraph> ;
.
# The location of the TDB dataset
:tdbDataset rdf:type tdb2:DatasetTDB2 ;
tdb2:location
"C:\\dev\\apache-jena-fuseki-3.8.0\\run/databases/weird7" ;
tdb2:unionDefaultGraph true ;
.
#### SERVER
...
[2019-01-31 13:54:58] Config INFO Load configuration:
file:///C:/dev/apache-jena-fuseki-3.10.0/run/configuration/weird7.ttl
[2019-01-31 13:54:58] Server ERROR Exception in initialization:
caught: Not in a transaction
[2019-01-31 13:54:58] WebAppContext WARN Failed startup of context
o.e.j.w.WebAppContext@6edc4161{Apache Jena Fuseki
Server,/,file:///C:/dev/apache-jena-fuseki-3.10.0/webapp/,UNAVAILABLE}
org.apache.jena.assembler.exceptions.AssemblerException: caught: Not
in a transaction
doing:
root:
file:///C:/dev/apache-jena-fuseki-3.10.0/run/configuration/weird7.ttl#model_inf
with type: http://jena.hpl.hp.com/2005/11/Assembler#InfModel assembler
class: class org.apache.jena.assembler.assemblers.InfModelAssembler
root: http://base/#dataset with type:
http://jena.hpl.hp.com/2005/11/Assembler#RDFDataset assembler class:
class org.apache.jena.sparql.core.assembler.DatasetAssembler
at
org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:165)
at
org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.open(AssemblerGroup.java:144)
at
org.apache.jena.assembler.assemblers.AssemblerGroup$ExpandingAssemblerGroup.open(AssemblerGroup.java:93)
at
org.apache.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:39)
at
org.apache.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:35)
at
org.apache.jena.assembler.assemblers.AssemblerGroup.openModel(AssemblerGroup.java:47)
at
org.apache.jena.sparql.core.assembler.DatasetAssembler.createDataset(DatasetAssembler.java:56)
at
org.apache.jena.sparql.core.assembler.DatasetAssembler.open(DatasetAssembler.java:43)
at
org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:157)
at
org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.open(AssemblerGroup.java:144)
at
org.apache.jena.assembler.assemblers.AssemblerGroup$ExpandingAssemblerGroup.open(AssemblerGroup.java:93)
at
org.apache.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:39)
at
org.apache.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:35)
at
org.apache.jena.fuseki.build.FusekiConfig.getDataset(FusekiConfig.java:345)
at
org.apache.jena.fuseki.build.FusekiConfig.buildDataService(FusekiConfig.java:299)
at
org.apache.jena.fuseki.build.FusekiConfig.buildDataAccessPoint(FusekiConfig.java:289)
at
org.apache.jena.fuseki.build.FusekiConfig.readConfiguration(FusekiConfig.java:272)
at
org.apache.jena.fuseki.build.FusekiConfig.readConfigurationDirectory(FusekiConfig.java:251)
at
org.apache.jena.fuseki.webapp.FusekiWebapp.initializeDataAccessPoints(FusekiWebapp.java:226)
at
org.apache.jena.fuseki.webapp.FusekiServerListener.serverInitialization(FusekiServerListener.java:98)
at
org.apache.jena.fuseki.webapp.FusekiServerListener.contextInitialized(FusekiServerListener.java:56)
at
org.eclipse.jetty.server.handler.ContextHandler.callContextInitialized(ContextHandler.java:952)
at
org.eclipse.jetty.servlet.ServletContextHandler.callContextInitialized(ServletContextHandler.java:558)
at
org.eclipse.jetty.server.handler.ContextHandler.startContext(ContextHandler.java:917)
at
org.eclipse.jetty.servlet.ServletContextHandler.startContext(ServletContextHandler.java:370)
at
org.eclipse.jetty.webapp.WebAppContext.startWebapp(WebAppContext.java:1497)
at
org.eclipse.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1459)
at
org.eclipse.jetty.server.handler.ContextHandler.doStart(ContextHandler.java:847)
at
org.eclipse.jetty.servlet.ServletContextHandler.doStart(ServletContextHandler.java:287)
at
org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:545)
at
org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
at
org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:138)
at
org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:108)
at
org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:113)
at
org.eclipse.jetty.server.handler.gzip.GzipHandler.doStart(GzipHandler.java:410)
at
org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
at
org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:138)
at org.eclipse.jetty.server.Server.start(Server.java:416)
at
org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:108)
at
org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:113)
at org.eclipse.jetty.server.Server.doStart(Server.java:383)
at
org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
at
org.apache.jena.fuseki.cmd.JettyFusekiWebapp.start(JettyFusekiWebapp.java:138)
at
org.apache.jena.fuseki.cmd.FusekiCmd.runFuseki(FusekiCmd.java:372)
at
org.apache.jena.fuseki.cmd.FusekiCmd$FusekiCmdInner.exec(FusekiCmd.java:356)
at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
at
org.apache.jena.fuseki.cmd.FusekiCmd$FusekiCmdInner.innerMain(FusekiCmd.java:104)
at org.apache.jena.fuseki.cmd.FusekiCmd.main(FusekiCmd.java:67)
Caused by: org.apache.jena.dboe.transaction.txn.TransactionException:
Not in a transaction
at
org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
at
org.apache.jena.dboe.trans.bplustree.BPlusTree.getRootRead(BPlusTree.java:159)
at
org.apache.jena.dboe.trans.bplustree.BPlusTree.find(BPlusTree.java:239)
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative.accessIndex(NodeTableNative.java:133)
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative._idForNode(NodeTableNative.java:118)
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeIdForNode(NodeTableNative.java:57)
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache._idForNode(NodeTableCache.java:222)
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeIdForNode(NodeTableCache.java:114)
at
org.apache.jena.tdb2.store.nodetable.NodeTableWrapper.getNodeIdForNode(NodeTableWrapper.java:47)
at
org.apache.jena.tdb2.store.nodetable.NodeTableInline.getNodeIdForNode(NodeTableInline.java:58)
at
org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.idForNode(NodeTupleTableConcrete.java:182)
at
org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.findAsNodeIds(NodeTupleTableConcrete.java:136)
at
org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.find(NodeTupleTableConcrete.java:114)
at
org.apache.jena.tdb2.store.DatasetPrefixesTDB.readPrefixMap(DatasetPrefixesTDB.java:111)
at
org.apache.jena.sparql.graph.GraphPrefixesProjection.getNsPrefixMap(GraphPrefixesProjection.java:94)
at
org.apache.jena.tdb2.store.GraphViewSwitchable$PrefixMappingImplTDB2.getNsPrefixMap(GraphViewSwitchable.java:159)
at
org.apache.jena.shared.impl.PrefixMappingImpl.setNsPrefixes(PrefixMappingImpl.java:138)
at
org.apache.jena.tdb2.store.GraphViewSwitchable.createPrefixMapping(GraphViewSwitchable.java:68)
at
org.apache.jena.graph.impl.GraphBase.getPrefixMapping(GraphBase.java:165)
at
org.apache.jena.reasoner.BaseInfGraph.getPrefixMapping(BaseInfGraph.java:55)
at
org.apache.jena.rdf.model.impl.ModelCom.getPrefixMapping(ModelCom.java:1018)
at
org.apache.jena.rdf.model.impl.ModelCom.setNsPrefixes(ModelCom.java:1055)
at
org.apache.jena.assembler.assemblers.ModelAssembler.open(ModelAssembler.java:45)
at
org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:157)
... 49 more
[2019-01-31 13:54:58] Server INFO Started 2019/01/31 13:54:58 GMT
on port 3030
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