Stuart - quick question - and from code review, not use test running ...
What was the update? Could it be that there was a syntax error in it?
Andy
On 27/08/13 18:16, Stuart Taylor wrote:
Hi all,
I'm having some more problems with Fuseki and full text search. I have
an InfModel backed by a TDB dataset, which I've added a Lucene text
index to. I'm having problems with updates and select queries resulting
in exceptions being thrown by Fuseki.
I am running Fuseki 0.2.8-SNAPSHOT 20130826-0756 which should include
the fixes for JENA-522 (where I was having problems earlier).
Unfortunately I haven't managed to come up with a complete running
example which reproduces the problem, but while I do that the stack
traces from Fuseki's log might be able to shed some light on what is
happening. I have also added the assembler file for my Fuseki set up at
the end of this message.
After some SPARQL Update queries I occasionally get:
17:43:33 WARN DatasetGraphText :: Exception in abort: Can't abort a
write lock-transaction
com.hp.hpl.jena.sparql.JenaTransactionException: Can't abort a write
lock-transaction
at
com.hp.hpl.jena.sparql.core.DatasetGraphWithLock._abort(DatasetGraphWithLock.java:100)
at
com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.abort(DatasetGraphTrackActive.java:56)
at
org.apache.jena.query.text.DatasetGraphText.abort(DatasetGraphText.java:139)
at
org.apache.jena.fuseki.servlets.HttpAction.abort(HttpAction.java:142)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:248)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.executeForm(SPARQL_Update.java:212)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:110)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:184)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeAction(SPARQL_ServletBase.java:165)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.execCommonWorker(SPARQL_ServletBase.java:153)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:73)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.doPost(SPARQL_Update.java:80)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:755)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at
org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:457)
at
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:229)
at
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1075)
at
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:384)
at
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
at
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1009)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at
org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:489)
at
org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:53)
at
org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:960)
at
org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1021)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
at
org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
at
org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:72)
at
org.eclipse.jetty.server.nio.BlockingChannelConnector$BlockingChannelEndPoint.run(BlockingChannelConnector.java:298)
at
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
at
org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
at java.lang.Thread.run(Thread.java:722)
17:43:33 WARN HttpAction :: Transaction still active in
endWriter - no commit or abort seen (forced abort)
17:43:33 WARN DatasetGraphText :: Exception in abort: this
IndexWriter is closed
org.apache.lucene.store.AlreadyClosedException: this IndexWriter is closed
at org.apache.lucene.index.IndexWriter.ensureOpen(IndexWriter.java:614)
at org.apache.lucene.index.IndexWriter.ensureOpen(IndexWriter.java:628)
at org.apache.lucene.index.IndexWriter.rollback(IndexWriter.java:1974)
at
org.apache.jena.query.text.TextIndexLucene.abortIndexing(TextIndexLucene.java:107)
at
org.apache.jena.query.text.DatasetGraphText.abort(DatasetGraphText.java:137)
at
org.apache.jena.fuseki.servlets.HttpAction.endWrite(HttpAction.java:153)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:257)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.executeForm(SPARQL_Update.java:212)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.perform(SPARQL_Update.java:110)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:184)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeAction(SPARQL_ServletBase.java:165)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.execCommonWorker(SPARQL_ServletBase.java:153)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:73)
at
org.apache.jena.fuseki.servlets.SPARQL_Update.doPost(SPARQL_Update.java:80)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:755)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at
org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:457)
at
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:229)
at
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1075)
at
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:384)
at
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
at
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1009)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at
org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:489)
at
org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:53)
at
org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:960)
at
org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1021)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
at
org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
at
org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:72)
at
org.eclipse.jetty.server.nio.BlockingChannelConnector$BlockingChannelEndPoint.run(BlockingChannelConnector.java:298)
at
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
at
org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
at java.lang.Thread.run(Thread.java:722)
Then running SELECT queries shortly after results in:
17:46:23 WARN Fuseki :: [13] RC = 500 : Iterator: started
at 24, now 30
java.util.ConcurrentModificationException: Iterator: started at 24, now 30
at
com.hp.hpl.jena.tdb.sys.DatasetControlMRSW.policyError(DatasetControlMRSW.java:157)
at
com.hp.hpl.jena.tdb.sys.DatasetControlMRSW.access$000(DatasetControlMRSW.java:32)
at
com.hp.hpl.jena.tdb.sys.DatasetControlMRSW$IteratorCheckNotConcurrent.checkCourrentModification(DatasetControlMRSW.java:110)
at
com.hp.hpl.jena.tdb.sys.DatasetControlMRSW$IteratorCheckNotConcurrent.hasNext(DatasetControlMRSW.java:118)
at org.apache.jena.atlas.iterator.Iter$4.hasNext(Iter.java:312)
at org.apache.jena.atlas.iterator.Iter$4.hasNext(Iter.java:312)
at org.apache.jena.atlas.iterator.Iter$4.hasNext(Iter.java:312)
at org.apache.jena.atlas.iterator.Iter.hasNext(Iter.java:910)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
at
com.hp.hpl.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:103)
at
com.hp.hpl.jena.util.iterator.NiceIterator$1.hasNext(NiceIterator.java:103)
at
com.hp.hpl.jena.reasoner.rulesys.impl.TopLevelTripleMatchFrame.nextMatch(TopLevelTripleMatchFrame.java:55)
at
com.hp.hpl.jena.reasoner.rulesys.impl.LPInterpreter.run(LPInterpreter.java:330)
at
com.hp.hpl.jena.reasoner.rulesys.impl.LPInterpreter.next(LPInterpreter.java:192)
at
com.hp.hpl.jena.reasoner.rulesys.impl.Generator.pump(Generator.java:250)
at
com.hp.hpl.jena.reasoner.rulesys.impl.Generator.pump(Generator.java:237)
at
com.hp.hpl.jena.reasoner.rulesys.impl.LPBRuleEngine.pump(LPBRuleEngine.java:308)
at
com.hp.hpl.jena.reasoner.rulesys.impl.LPTopGoalIterator.moveForward(LPTopGoalIterator.java:109)
at
com.hp.hpl.jena.reasoner.rulesys.impl.LPTopGoalIterator.hasNext(LPTopGoalIterator.java:222)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
at
com.hp.hpl.jena.util.iterator.FilterIterator.hasNext(FilterIterator.java:54)
at
com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
at
com.hp.hpl.jena.util.iterator.FilterIterator.hasNext(FilterIterator.java:54)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIterTriplePattern$TripleMapper.hasNextBinding(QueryIterTriplePattern.java:151)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:81)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIterBlockTriples.hasNextBinding(QueryIterBlockTriples.java:64)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:40)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:40)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:40)
at
com.hp.hpl.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:112)
at
com.hp.hpl.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStream.java:75)
at
com.hp.hpl.jena.sparql.resultset.ResultSetMem.<init>(ResultSetMem.java:97)
at
com.hp.hpl.jena.query.ResultSetFactory.makeRewindable(ResultSetFactory.java:420)
at
com.hp.hpl.jena.sparql.resultset.TextOutput.write(TextOutput.java:149)
at
com.hp.hpl.jena.sparql.resultset.TextOutput.write(TextOutput.java:132)
at
com.hp.hpl.jena.sparql.resultset.TextOutput.write(TextOutput.java:120)
at
com.hp.hpl.jena.sparql.resultset.TextOutput.format(TextOutput.java:67)
at
com.hp.hpl.jena.query.ResultSetFormatter.out(ResultSetFormatter.java:135)
at
org.apache.jena.fuseki.servlets.ResponseResultSet$3.output(ResponseResultSet.java:238)
at
org.apache.jena.fuseki.servlets.ResponseResultSet.output(ResponseResultSet.java:283)
at
org.apache.jena.fuseki.servlets.ResponseResultSet.textOutput(ResponseResultSet.java:244)
at
org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet$(ResponseResultSet.java:145)
at
org.apache.jena.fuseki.servlets.ResponseResultSet.doResponseResultSet(ResponseResultSet.java:88)
at
org.apache.jena.fuseki.servlets.SPARQL_Query.sendResults(SPARQL_Query.java:348)
at
org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:244)
at
org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:195)
at
org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:80)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:184)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeAction(SPARQL_ServletBase.java:165)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.execCommonWorker(SPARQL_ServletBase.java:153)
at
org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:73)
at
org.apache.jena.fuseki.servlets.SPARQL_Query.doGet(SPARQL_Query.java:61)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:735)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at
org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1448)
at
org.eclipse.jetty.servlets.UserAgentFilter.doFilter(UserAgentFilter.java:82)
at org.eclipse.jetty.servlets.GzipFilter.doFilter(GzipFilter.java:294)
at
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1419)
at
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:455)
at
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:229)
at
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1075)
at
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:384)
at
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
at
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1009)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at
org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:489)
at
org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:53)
at
org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:949)
at
org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1011)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
at
org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
at
org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:72)
at
org.eclipse.jetty.server.nio.BlockingChannelConnector$BlockingChannelEndPoint.run(BlockingChannelConnector.java:298)
at
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
at
org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
at java.lang.Thread.run(Thread.java:722)
17:46:23 INFO Fuseki :: [13] 500 Iterator: started at 24,
now 30 (25 ms)
Here is the assembler file:
@prefix : <#> .
@prefix fuseki:
<http://jena.apache.org/fuseki#><http://jena.apache.org/fuseki#> .
@prefix rdf:
<http://www.w3.org/1999/02/22-rdf-syntax-ns#><http://www.w3.org/1999/02/22-rdf-syntax-ns#>
.
@prefix rdfs:
<http://www.w3.org/2000/01/rdf-schema#><http://www.w3.org/2000/01/rdf-schema#>
.
@prefix tdb:
<http://jena.hpl.hp.com/2008/tdb#><http://jena.hpl.hp.com/2008/tdb#> .
@prefix ja:
<http://jena.hpl.hp.com/2005/11/Assembler#><http://jena.hpl.hp.com/2005/11/Assembler#>
.
@prefix text:
<http://jena.apache.org/text#><http://jena.apache.org/text#> .
@prefix dc: <http://purl.org/dc/terms/><http://purl.org/dc/terms/> .
[] rdf:type fuseki:Server ;
# Timeout - server-wide default: milliseconds.
# Format 1: "1000" -- 1 second timeout
# Format 2: "10000,60000" -- 10s timeout to first result, then 60s
timeout to for rest of query.
# See java doc for ARQ.queryTimeout
ja:context [ ja:cxtName "arq:queryTimeout" ; ja:cxtValue
"12000,50000" ] ;
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 .
## Initialize text query
[] ja:loadClass "org.apache.jena.query.text.TextQuery" .
# A TextDataset is a regular dataset with a text index.
text:TextDataset rdfs:subClassOf ja:RDFDataset .
# Lucene index
text:TextIndexLucene rdfs:subClassOf text:TextIndex .
## ---------------------------------------------------------------
## Service with only SPARQL query on an inference model.
## Inference model bbase data in TDB.
<#service1> rdf:type fuseki:Service ;
rdfs:label "TDB/text service" ;
fuseki:name "dataset" ; # http://host/dataset
fuseki:serviceQuery "query" ;
fuseki:serviceUpdate "update" ;
fuseki:serviceUpload "upload" ;
fuseki:serviceReadWriteGraphStore "data" ;
fuseki:serviceReadGraphStore "get" ;
fuseki:dataset <#dataset_fulltext> ;
.
<#dataset_inf> rdf:type ja:RDFDataset ;
ja:defaultGraph <#model_inf> .
<#model_inf> rdf:type ja:Model ;
ja:baseModel <#tdbGraph> ;
ja:reasoner [ ja:reasonerURL
<http://jena.hpl.hp.com/2003/OWLMicroFBRuleReasoner><http://jena.hpl.hp.com/2003/OWLMicroFBRuleReasoner>
] .
<#tdbDataset> rdf:type tdb:DatasetTDB ;
tdb:location "Data" .
<#tdbGraph> rdf:type tdb:GraphTDB ;
tdb:dataset <#tdbDataset> .
# Dataset with full text index.
<#dataset_fulltext> rdf:type text:TextDataset ;
text:dataset <#dataset_inf> ;
##text:dataset <#tdbDataset> ;
text:index <#indexLucene> .
# Text index description
<#indexLucene> a text:TextIndexLucene ;
text:directory <file:Lucene><file:Lucene> ;
##text:directory "mem" ;
text:entityMap <#entMap> ;
.
# Mapping in the index
# URI stored in field "uri"
# rdfs:label is mapped to field "text"
<#entMap> a text:EntityMap ;
text:entityField "uri" ;
text:defaultField "text" ;
text:map (
[ text:field "text" ; text:predicate dc:title ]
[ text:field "text" ; text:predicate dc:description ]
) .
Any advice appreciated!
Thanks,
Stuart.
The University of Aberdeen is a charity registered in Scotland, No
SC013683.
