Fuseki 500 Error: DatasetGraph.delete (Quad)

Question

I installed the Fuseki endpoint with the hope of getting into the Jena SDB database (truly the MySQL database in the backend) with some SPARQL, both for selecting and for updating / deleting queries. The SPARQL select query works fine, but whenever I try to run an update request, 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 launched 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 & 

Access to 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 could be causing this? Below is the FusekiLog file, if useful. 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) 

Answer 1

You seem to be working

 Fuseki - version 0.2.2-incubating-SNAPSHOT 

despite

 export FusekiInstallDir=/data/jena-fuseki-0.2.4 

This may be a known bug, which is now fixed. Could you upgrade to 0.2.5?

Configuration says:

 jumble:SDBConnect rdfs:subClassOf ja:RDFDataset . 

but

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

therefore jumble:SDBConnect not a data set (it does not matter - the code follows the link <#VIVOStore>

No

 sdb:DatasetStore rdfs:subClassOf ja:RDFDataset . 

but your local init class can do something here.

Answer 2

tdb.lock exists, you need to delete this file Use the following command to delete this file

 rm -f run/system/tdb.lock