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I have set up a Fuseki endpoint with the hopes of hitting a Jena SDB database (Truly a MySQL database in the backend) with some SPARQL, both select and update/delete queries. SPARQL select queries work just fine, but whenever I try and run an update query such as insert or delete, I get the following from Fuseki:

Error 500: DatasetGraph.delete(Quad)


Fuseki - version 0.2.6-SNAPSHOT (Build date: 2012-12-06T08:26:37-0500)

I have started up my endpoint by running the following script:

#!/bin/bash

 export FusekiInstallDir=/data/jena-fuseki-0.2.6-SNAPSHOT
 export FusekiPort=3030
 export FusekiJVMArgs="-cp ./fuseki-server.jar:lib/ReconnectingSDB-0.1-SNAPSHOT.jar:lib/jena-sdb-1.3.6-SNAPSHOT.jar:lib/mysql-connector-java-5.1.16-bin.jar:lib/jena-arq-2.9.5-SNAPSHOT.jar  -Xmx768M"
 export Date=`date +%Y-%m-%d`
 export FusekiLogFile=$FusekiInstallDir/FusekiLog-$Date.log
 export FusekiConfigFile=$FusekiInstallDir/fuseki.ttl
 export FusekiServiceName=/VIVO

 # Check to see if logfile exists
 if [ ! -f $FusekiLogFile ]; then
    touch $FusekiLogFile
 fi

 # Check to see if config file exists
 if [ ! -f $FusekiConfigFile ]; then
    echo “ERROR – Fuseki failed to start – no configuration file - $FusekiConfigFile” >> $FusekiLogFile
    exit 1
 fi

 # Execute Java calling the package for Fuseki
 java $FusekiJVMArgs org.apache.jena.fuseki.FusekiCmd --desc $FusekiConfigFile --update --port=$FusekiPort $FusekiServiceName >> $FusekiLogFile 2>&1 &

Which accesses the following configuration file (fuseki.ttl):

@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 sdb:      <http://jena.hpl.hp.com/2007/sdb#> .
@prefix ja:      <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix jumble:   <http://rootdev.net/vocab/jumble#> .
@prefix :        <#> .

[] rdf:type fuseki:Server ;
   # Services available.  Only explicitly listed services are configured.
   #  If there is a service description not linked from this list, it is ignored.
   fuseki:services (
     <#service1>
   ) .
# Declaration additional assembler items.
# [] ja:loadClass "com.hp.hpl.jena.tdb.TDB" .
[] ja:loadClass "net.rootdev.fusekisdbconnect.SDBConnect" .

jumble:SDBConnect rdfs:subClassOf ja:RDFDataset .

<#dataset> rdf:type jumble:SDBConnect  ;
   rdfs:label "SDB" ;
   sdb:layout "layout2" ;
   jumble:defaultUnionGraph "true" ; # will switch option on globally, in fact
   sdb:connection [
     rdf:type sdb:SDBConnection ;
     # Using MySQL
     sdb:sdbHost        "LASP-DB-DEV" ;
     sdb:sdbType        "MySQL" ;
     sdb:sdbName        "db" ;
     sdb:sdbUser        "user" ;
     sdb:sdbPassword    "pass" ;
     sdb:driver "com.mysql.jdbc.Driver" ;
     #sdb:jdbcUrl       "jdbc:mysql://localhost/vivodb?autoReconnect=true"
    ] ;
  .
## ---------------------------------------------------------------
## Vivo dataset in sdb

<#service1> rdf:type fuseki:Service ;
    fuseki:name                       "VIVO" ;       # http://host:port/ds
    fuseki:serviceQuery               "query" ;    # SPARQL query service
    fuseki:serviceQuery               "sparql" ;    # SPARQL query service
        fuseki:serviceUpdate                      "update" ;
    # A separate ead-only graph store endpoint:
    fuseki:serviceReadGraphStore      "get" ;      # SPARQL Graph store protocol (read only)
    fuseki:dataset                   <#dataset> ;
    .

Does anyone have any ideas on what might be causing this? Below is the resulting FusekiLog file if that is helpful. Thanks in advance!

12:32:40 INFO  Server               :: Dataset from assembler
12:32:40 WARN  SDBConnect           :: Hooking in to update and query engines
12:32:40 WARN  SDBConnect           :: Hooking in to assemblers
12:32:40 WARN  SDBConnect           :: Hooking in to assemblers
12:32:41 INFO  Server               :: Dataset path = /VIVO
12:32:41 INFO  Server               :: Fuseki 0.2.6-SNAPSHOT 2012-12-06T08:26:37-0500
12:32:41 INFO  Server               :: Started 2013/03/20 12:32:41 MDT on port 3030
12:32:52 INFO  Fuseki               :: [1] GET http://sorce-dp2:3030/VIVO/query?query=PREFIX+rdf%3A+++%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0D%0APREFIX+rdfs%3A++%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0D%0APREFIX+xsd%3A+++%3Chttp%3A%2F%2Fwww.w3.org%2F2001%2FXMLSchema%23%3E%0D%0APREFIX+owl%3A+++%3Chttp%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23%3E%0D%0APREFIX+swrl%3A++%3Chttp%3A%2F%2Fwww.w3.org%2F2003%2F11%2Fswrl%23%3E%0D%0APREFIX+swrlb%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2003%2F11%2Fswrlb%23%3E%0D%0APREFIX+vitro%3A+%3Chttp%3A%2F%2Fvitro.mannlib.cornell.edu%2Fns%2Fvitro%2F0.7%23%3E%0D%0APREFIX+bibo%3A+%3Chttp%3A%2F%2Fpurl.org%2Fontology%2Fbibo%2F%3E%0D%0APREFIX+dcelem%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Felements%2F1.1%2F%3E%0D%0APREFIX+dcterms%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0D%0APREFIX+event%3A+%3Chttp%3A%2F%2Fpurl.org%2FNET%2Fc4dm%2Fevent.owl%23%3E%0D%0APREFIX+foaf%3A+%3Chttp%3A%2F%2Fxmlns.com%2Ffoaf%2F0.1%2F%3E%0D%0APREFIX+geo%3A+%3Chttp%3A%2F%2Faims.fao.org%2Faos%2Fgeopolitical.owl%23%3E%0D%0APREFIX+pvs%3A+%3Chttp%3A%2F%2Fvivoweb.org%2Fontology%2Fprovenance-support%23%3E%0D%0APREFIX+ero%3A+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2F%3E%0D%0APREFIX+scires%3A+%3Chttp%3A%2F%2Fvivoweb.org%2Fontology%2Fscientific-research%23%3E%0D%0APREFIX+skos%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23%3E%0D%0APREFIX+vitro-public%3A+%3Chttp%3A%2F%2Fvitro.mannlib.cornell.edu%2Fns%2Fvitro%2Fpublic%23%3E%0D%0APREFIX+vivo%3A+%3Chttp%3A%2F%2Fvivoweb.org%2Fontology%2Fcore%23%3E%0D%0APREFIX+laspcms%3A+%3Chttp%3A%2F%2Fsorce-dp2%3A8080%2Flaspcms%2F%3E%0D%0APREFIX+vsto%3A+%3Chttp%3A%2F%2Fescience.rpi.edu%2Fontology%2Fvsto%2F2%2F0%2Fvsto.owl%23%3E%0D%0A%0D%0ASELECT+%3Fname%0D%0AWHERE%0D%0A%7B%0D%0A%3Fthing+a+vsto%3ADataset+.%0D%0A%3Fthing+rdfs%3Alabel+%3Fname%0D%0A%7D%0D%0A&output=text&stylesheet=%2Fxml-to-html.xsl
12:32:52 INFO  Fuseki               :: [1] Query = PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>  PREFIX rdfs:  <http://www.w3.org/2000/01/rdf-schema#>  PREFIX xsd:   <http://www.w3.org/2001/XMLSchema#>  PREFIX owl:   <http://www.w3.org/2002/07/owl#>  PREFIX swrl:  <http://www.w3.org/2003/11/swrl#>  PREFIX swrlb: <http://www.w3.org/2003/11/swrlb#>  PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>  PREFIX bibo: <http://purl.org/ontology/bibo/>  PREFIX dcelem: <http://purl.org/dc/elements/1.1/>  PREFIX dcterms: <http://purl.org/dc/terms/>  PREFIX event: <http://purl.org/NET/c4dm/event.owl#>  PREFIX foaf: <http://xmlns.com/foaf/0.1/>  PREFIX geo: <http://aims.fao.org/aos/geopolitical.owl#>  PREFIX pvs: <http://vivoweb.org/ontology/provenance-support#>  PREFIX ero: <http://purl.obolibrary.org/obo/>  PREFIX scires: <http://vivoweb.org/ontology/scientific-research#>  PREFIX skos: <http://www.w3.org/2004/02/skos/core#>  PREFIX vitro-public: <http://vitro.mannlib.cornell.edu/ns/vitro/public#>  PREFIX vivo: <http://vivoweb.org/ontology/core#>  PREFIX laspcms: <http://sorce-dp2:8080/laspcms/>  PREFIX vsto: <http://escience.rpi.edu/ontology/vsto/2/0/vsto.owl#>    SELECT ?name  WHERE  {  ?thing a vsto:Dataset .  ?thing rdfs:label ?name  }
12:32:52 INFO  Fuseki               :: [1] OK/select
12:32:52 INFO  Fuseki               :: [1] 200 OK
12:35:06 INFO  Fuseki               :: [2] POST http://sorce-dp2:3030/VIVO/update
12:35:06 WARN  SPARQL_Update$HttpActionUpdate :: Transaction still active in endWriter - no commit or abort seen (forced abort)
12:35:06 WARN  SPARQL_Update$HttpActionUpdate :: Exception in forced abort (trying to continue)
com.hp.hpl.jena.sparql.core.DatasetGraphWithLock$JenaLockException: Can't abort a locked update
        at com.hp.hpl.jena.sparql.core.DatasetGraphWithLock._abort(DatasetGraphWithLock.java:97)
        at com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.abort(DatasetGraphTrackActive.java:63)
        at org.apache.jena.fuseki.servlets.HttpAction.endWrite(HttpAction.java:121)
        at org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:246)
        at org.apache.jena.fuseki.servlets.SPARQL_Update.executeForm(SPARQL_Update.java:232)
        at org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:118)
        at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommonWorker(SPARQL_ServletBase.java:117)
        at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:67)
        at org.apache.jena.fuseki.servlets.SPARQL_Update.doPost(SPARQL_Update.java:84)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
        at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:598)
        at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:442)
        at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
        at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1033)
        at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:369)
        at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:186)
        at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:967)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:129)
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:111)
        at org.eclipse.jetty.server.Server.handle(Server.java:358)
        at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:452)
        at org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:47)
        at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:894)
        at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:948)
        at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:851)
        at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
        at org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:66)
        at org.eclipse.jetty.server.nio.BlockingChannelConnector$BlockingChannelEndPoint.run(BlockingChannelConnector.java:293)
        at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:603)
        at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:538)
        at java.lang.Thread.run(Thread.java:662)
12:35:06 WARN  Fuseki               :: [2] RC = 500 : DatasetGraph.delete(Quad)
java.lang.UnsupportedOperationException: DatasetGraph.delete(Quad)
        at com.hp.hpl.jena.sparql.core.DatasetGraphBase.delete(DatasetGraphBase.java:81)
        at com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.delete(DatasetGraphTrackActive.java:131)
        at com.hp.hpl.jena.sparql.core.DatasetGraphWrapper.delete(DatasetGraphWrapper.java:76)
        at com.hp.hpl.jena.sparql.modify.UpdateEngineWorker.execDelete(UpdateEngineWorker.java:438)
        at com.hp.hpl.jena.sparql.modify.UpdateEngineWorker.visit(UpdateEngineWorker.java:357)
        at com.hp.hpl.jena.sparql.modify.request.UpdateModify.visit(UpdateModify.java:97)
        at com.hp.hpl.jena.sparql.modify.UpdateEngineMain.execute(UpdateEngineMain.java:57)
        at com.hp.hpl.jena.sparql.modify.UpdateProcessorBase.execute(UpdateProcessorBase.java:56)
        at com.hp.hpl.jena.update.UpdateAction.execute$(UpdateAction.java:334)
        at com.hp.hpl.jena.update.UpdateAction.execute(UpdateAction.java:327)
        at com.hp.hpl.jena.update.UpdateAction.execute(UpdateAction.java:307)
        at com.hp.hpl.jena.update.UpdateAction.execute(UpdateAction.java:257)
        at org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:242)
        at org.apache.jena.fuseki.servlets.SPARQL_Update.executeForm(SPARQL_Update.java:232)
        at org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:118)
        at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommonWorker(SPARQL_ServletBase.java:117)
        at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:67)
        at org.apache.jena.fuseki.servlets.SPARQL_Update.doPost(SPARQL_Update.java:84)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
        at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:598)
        at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:442)
        at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
        at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1033)
        at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:369)
        at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:186)
        at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:967)
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:129)
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:111)
        at org.eclipse.jetty.server.Server.handle(Server.java:358)
        at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:452)
        at org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:47)
        at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:894)
        at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:948)
        at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:851)
        at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
        at org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:66)
        at org.eclipse.jetty.server.nio.BlockingChannelConnector$BlockingChannelEndPoint.run(BlockingChannelConnector.java:293)
        at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:603)
        at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:538)
        at java.lang.Thread.run(Thread.java:662)
12:35:06 INFO  Fuseki               :: [2] 500 DatasetGraph.delete(Quad)
Mik Cox
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2 Answers2

0

You seem to be running 

Fuseki - version 0.2.2-incubating-SNAPSHOT

despite

export FusekiInstallDir=/data/jena-fuseki-0.2.4

It could be a known bug that is now fixed. Could you upgrade to 0.2.5?

The config says:

jumble:SDBConnect rdfs:subClassOf ja:RDFDataset .

but 

<#ufvivo_dataset_read> rdf:type      sdb:DatasetStore ;
    sdb:store <#VIVOStore>
   .
<#VIVOStore> rdf:type jumble:SDBConnect;

so jumble:SDBConnect is not a dataset (may not matter - the code follows the <#VIVOStore> link

There is no 

sdb:DatasetStore  rdfs:subClassOf  ja:RDFDataset .

but your local init class may do something here.

AndyS
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  • upgrading to 0.2.5 produces errors like: `Error 500: com.hp.hpl.jena.query.DatasetFactory.create(Lcom/hp/hpl/jena/sparql/core/DatasetGraph;)Lcom/hp/hpl/jena/query/DataSource;` And fusekilog gives NoSuchMethodError. This likely means I am missing some necessary library I would assume? – Mik Cox Dec 01 '12 at 00:55
  • I have also tried rolling back to a full jena-fuseki-0.2.2 with the libraries in the package and I get the original Error 500: DatasetGraph.delete(Quad) Fuseki - version 0.2.2-incubating-SNAPSHOT (Build date: 20120501-1232) – Mik Cox Dec 04 '12 at 00:34
  • I have updated to the newest available version of fuseki (0.2.6) and am getting the original error whenever I try and run any update query. Does anyone have any suggestions other than updating? I have updated the question with my new config file. – Mik Cox Mar 15 '13 at 18:13
  • There are no update operations on <#service1>. The configuration overrides the command line --update. With the editted question, I can't see what going on any more. Please add information, not replace it. What operation was before the POST? It looks like the setup in net.rootdev.fusekisdbconnect.SDBConnect is odd in some way. – AndyS Mar 19 '13 at 09:20
  • The update operation is indeed in my config file, I mistakenly copied the contents of the wrong file. The correct file has been attached, along with the resulting error code from the fuseki server. You can see the logs from when the server started. I successfully ran a select query against the sdb database, and then upon sending an update query the original error was again returned. – Mik Cox Mar 20 '13 at 18:40
0

there is tdb.lock exist, you need to remove this file Use the following command to remove that file

rm -f run/system/tdb.lock
Ahemd Hemaid
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