This occurred again on another server. There were no errors before this,
but many warnings on invalid data, if that is related. Now we get this
error on all operations.
12:57:42 WARN Fuseki :: [line: 149803, col: 81] Bad IRI:
<mailto:"Finskas> Code: 4/UNWISE_CHARACTER in PATH: The character
matches no grammar rules of URIs/IRIs. These characters are permitted in
RDF URI References, XML system identifiers, and XML Schema anyURIs.
...
14:48:28 WARN Fuseki :: [line: 475806, col: 80] Lexical form
'' not valid for datatype XSD boolean
...
14:52:06 WARN Fuseki :: [24] RC = 500 : NodeTableTRDF/Read
org.apache.jena.tdb2.TDBException: NodeTableTRDF/Read
at
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:52)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:206)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:131)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:52)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:65)
~[fuseki-server.jar:3.17.0]
at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:112)
~[fuseki-server.jar:3.17.0]
at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:108)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.tdb2.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:53)
~[fuseki-server.jar:3.17.0]
at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.atlas.iterator.IteratorWrapper.next(IteratorWrapper.java:36)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.dboe.transaction.txn.IteratorTxnTracker.next(IteratorTxnTracker.java:39)
~[fuseki-server.jar:3.17.0]
at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:352)
~[fuseki-server.jar:3.17.0]
at org.apache.jena.atlas.iterator.Iter.next(Iter.java:1072)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.mem.TrackingTripleIterator.next(TrackingTripleIterator.java:47)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.mem.TrackingTripleIterator.next(TrackingTripleIterator.java:31)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIterTriplePattern$TripleMapper.hasNextBinding(QueryIterTriplePattern.java:145)
~[fuseki-s erver.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:74)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIterBlockTriplesStar.hasNextBinding(QueryIterBlockTriplesStar.java:54)
~[fuseki-server.ja r:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIterGroup$1.initializeIterator(QueryIterGroup.java:82)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.atlas.iterator.IteratorDelayedInitialization.init(IteratorDelayedInitialization.java:40)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.atlas.iterator.IteratorDelayedInitialization.hasNext(IteratorDelayedInitialization.java:50)
~[fuseki-server.jar:3.17. 0]
at
org.apache.jena.sparql.engine.iterator.QueryIterPlainWrapper.hasNextBinding(QueryIterPlainWrapper.java:53)
~[fuseki-server.jar:3.17.0 ]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIterProcessBinding.hasNextBinding(QueryIterProcessBinding.java:66)
~[fuseki-server.jar:3. 17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIterConvert.hasNextBinding(QueryIterConvert.java:58)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:38)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorWrapper.hasNextBinding(QueryIteratorWrapper.java:38)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.ResultSetStream.hasNext(ResultSetStream.java:74)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.sparql.engine.ResultSetCheckCondition.hasNext(ResultSetCheckCondition.java:55)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.executeQuery(SPARQLQueryProcessor.java:324)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.execute(SPARQLQueryProcessor.java:273)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.executeBody(SPARQLQueryProcessor.java:233)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.execute(SPARQLQueryProcessor.java:213)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:58)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.SPARQLQueryProcessor.execPost(SPARQLQueryProcessor.java:83)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.ActionProcessor.process(ActionProcessor.java:34)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.ActionBase.process(ActionBase.java:55)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.ActionExecLib.execAction(ActionExecLib.java:106)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.server.Dispatcher.dispatchAction(Dispatcher.java:118)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.server.Dispatcher.process(Dispatcher.java:110)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.server.Dispatcher.dispatch(Dispatcher.java:96)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:51)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:450)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
~[fuseki-server.jar:3.17.0]
at
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:284)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.fuseki.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:247)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:602)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1612)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1582)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:716)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
~[fuseki-server.jar:3.17.0]
at org.eclipse.jetty.server.Server.handle(Server.java:516)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:383)
~[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:556)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:375)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:273)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:336)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:313)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:171)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:129)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:375)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:773)
[fuseki-server.jar:3.17.0]
at
org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:905)
[fuseki-server.jar:3.17.0]
at java.lang.Thread.run(Thread.java:832) [?:?]
Caused by: org.apache.thrift.protocol.TProtocolException: Unrecognized
type 0
at
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:144)
~[fuseki-server.jar:3.17.0]
at
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:60)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:433)
~[fuseki-server.jar:3.17.0]
at
org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224)
~[fuseki-server.jar:3.17.0]
at
org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213)
~[fuseki-server.jar:3.17.0]
at org.apache.thrift.TUnion.read(TUnion.java:138)
~[fuseki-server.jar:3.17.0]
at
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:82)
~[fuseki-server.jar:3.17.0]
... 108 more
14:52:06 INFO Fuseki :: [24] 500 Server Error (12 ms)
On 27/04/2021 13.22, Andy Seaborne wrote:
On 27/04/2021 09:59, Mikael Pesonen wrote:
That's our guess too, but would be nice to have some idea where to
look for the cause. Does Jena/Fuseki handle disk full situations
without corruption?
It should do (the transaction aborts) which is why I was asking.
Bulk loading, other than loader "basic" which is safe - depends
exactly when it happens in the process i.e. no guarantees.
Andy
On 27/04/2021 11.56, Andy Seaborne wrote:
In the original message,
There was shortage of disk space, hope the db is not corrupted.
What happened?
This is the only thing you've mentioned that relates to update.
Everything else is "read" and the fault occurred at an earlier time
or its an environmental factor (one mentioned file access
permissions e.g. another process is interfering with files).
Apr 12 12:30:55 solid java[22910]: [2021-04-12 12:30:55] Fuseki
WARN [346] RC = 500 : a fault occurred in a recent unsafe memory
access operation in compiled Java code Apr 12 12:30:55 solid
java[22910]: at
org.apache.jena.dboe.base.buffer.RecordBuffer.compare(RecordBuffer.java:192)
~[fuseki-server.jar:3.17.0]
so JDK ByteBuffer.get failed bu works almost always. It is likely to
be an environmental factor (the file system, background process
messing around, hardware issue).
Andy
--
Lingsoft - 30 years of Leading Language Management
www.lingsoft.fi
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Mikael Pesonen
System Engineer
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