subject:"Re\: NodeTableTRDF\/Read exception"

Re: NodeTableTRDF/Read exception

2023-06-19 Thread Mikael Pesonen

Before that there are few occasions of quite heavy way to handle missing 
graph in CLEAR GRAPH. Maybe something going on there?


Jun 19 11:35:22 xxx.fi java[1047205]: [2023-06-19 11:35:22] Fuseki 
INFO  [34] POST http://xxx.fi/ds
Jun 19 11:35:22 xxx.fi java[1047205]: [2023-06-19 11:35:22] Fuseki 
INFO  [34] Update
Jun 19 11:35:22 xxx.fi java[1047205]: [2023-06-19 11:35:22] Fuseki 
WARN  [34] ActionErrorException with cause
Jun 19 11:35:22 xxx.fi java[1047205]: 
org.apache.jena.fuseki.servlets.ActionErrorException: No such graph: 
http://www.yso.fi/onto/mesh/
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.ServletOps.errorOccurred(ServletOps.java:275) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:259) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.SPARQL_Update.executeBody(SPARQL_Update.java:191) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.SPARQL_Update.execute(SPARQL_Update.java:106) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.ActionService.executeLifecycle(ActionService.java:58) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.SPARQL_Update.execPost(SPARQL_Update.java:91) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.ActionProcessor.process(ActionProcessor.java:34) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.ActionBase.process(ActionBase.java:54) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.ActionExecLib.execActionSub(ActionExecLib.java:124) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.ActionExecLib.execAction(ActionExecLib.java:98) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.server.Dispatcher.dispatchAction(Dispatcher.java:164) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.server.Dispatcher.process(Dispatcher.java:156) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.server.Dispatcher.dispatch(Dispatcher.java:83) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:48) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:202) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1635) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:450) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) 
~[fuseki-server.jar:4.6.1]
Jun 19 11:35:22 xxx.fi java[1047205]: at 
org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) 
~[fuseki

Re: NodeTableTRDF/Read exception

2023-06-19 Thread Mikael Pesonen

I deleted jena data folder, restarted db and started reinputting data. 
Still after a while I get NodeTableTRDF/Read. Any idea?


On 21/03/2022 20.43, Andy Seaborne wrote:
The only time I have seen anything similar to this is on Android where 
something other process is messing about the files. TDB is not proof 
again other processes accessing the same files, including with shared 
network drives where different computers access the same filesystem.


    Andy

On 21/03/2022 11:39, Mikael Pesonen wrote:


Got this again after few days of little usage after TDB2 was rebuilt 
from empty. Would you suggest this is hw error? No possibility that 
its Jena error?


On 28/05/2021 17.25, Andy Seaborne wrote:



On 28/05/2021 14:59, Mikael Pesonen wrote:


I should try some older Jena/Fuseki version?


Yes.

Also
 - run on different hardware.
 - run multiple times
 - look at the data and see if anything unusual is in it.
 etc etc




On 28/05/2021 16.49, Andy Seaborne wrote:



On 28/05/2021 14:03, Mikael Pesonen wrote:


No this is the fresh db, started from empty today. And plenty of 
disk space.


So it's repeatble.

With no Minimal, Verifiable, Complete Example, it'll have to be an 
on-site investigation. Try different versions.


    Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of 
turtle, imported without warnings this time, but reading the 
graph fails with this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar

Re: NodeTableTRDF/Read exception

2023-05-15 Thread Mikael Pesonen


Normal updates work but this comes with clear graph.

On 12/05/2023 14.58, Mikael Pesonen wrote:
Got this NodeTableTRDF/Read again in our production environment. I got 
message from admin that Jena had unusually high memory consumption and 
it suddenly normalized yesterday. Maybe it could be related to this.


On 21/03/2022 20.43, Andy Seaborne wrote:
The only time I have seen anything similar to this is on Android 
where something other process is messing about the files. TDB is not 
proof again other processes accessing the same files, including with 
shared network drives where different computers access the same 
filesystem.


    Andy

On 21/03/2022 11:39, Mikael Pesonen wrote:


Got this again after few days of little usage after TDB2 was rebuilt 
from empty. Would you suggest this is hw error? No possibility that 
its Jena error?


On 28/05/2021 17.25, Andy Seaborne wrote:



On 28/05/2021 14:59, Mikael Pesonen wrote:


I should try some older Jena/Fuseki version?


Yes.

Also
 - run on different hardware.
 - run multiple times
 - look at the data and see if anything unusual is in it.
 etc etc




On 28/05/2021 16.49, Andy Seaborne wrote:



On 28/05/2021 14:03, Mikael Pesonen wrote:


No this is the fresh db, started from empty today. And plenty of 
disk space.


So it's repeatble.

With no Minimal, Verifiable, Complete Example, it'll have to be 
an on-site investigation. Try different versions.


    Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of 
turtle, imported without warnings this time, but reading the 
graph fails with this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIterat

Re: NodeTableTRDF/Read exception

2023-05-12 Thread Mikael Pesonen

Got this NodeTableTRDF/Read again in our production environment. I got 
message from admin that Jena had unusually high memory consumption and 
it suddenly normalized yesterday. Maybe it could be related to this.


On 21/03/2022 20.43, Andy Seaborne wrote:
The only time I have seen anything similar to this is on Android where 
something other process is messing about the files. TDB is not proof 
again other processes accessing the same files, including with shared 
network drives where different computers access the same filesystem.


    Andy

On 21/03/2022 11:39, Mikael Pesonen wrote:


Got this again after few days of little usage after TDB2 was rebuilt 
from empty. Would you suggest this is hw error? No possibility that 
its Jena error?


On 28/05/2021 17.25, Andy Seaborne wrote:



On 28/05/2021 14:59, Mikael Pesonen wrote:


I should try some older Jena/Fuseki version?


Yes.

Also
 - run on different hardware.
 - run multiple times
 - look at the data and see if anything unusual is in it.
 etc etc




On 28/05/2021 16.49, Andy Seaborne wrote:



On 28/05/2021 14:03, Mikael Pesonen wrote:


No this is the fresh db, started from empty today. And plenty of 
disk space.


So it's repeatble.

With no Minimal, Verifiable, Complete Example, it'll have to be an 
on-site investigation. Try different versions.


    Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of 
turtle, imported without warnings this time, but reading the 
graph fails with this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.Q

Re: NodeTableTRDF/Read exception

2022-03-22 Thread Mikael Pesonen




We don't have that going on atleast.

On 21/03/2022 20.43, Andy Seaborne wrote:
The only time I have seen anything similar to this is on Android where 
something other process is messing about the files. TDB is not proof 
again other processes accessing the same files, including with shared 
network drives where different computers access the same filesystem.


    Andy

On 21/03/2022 11:39, Mikael Pesonen wrote:


Got this again after few days of little usage after TDB2 was rebuilt 
from empty. Would you suggest this is hw error? No possibility that 
its Jena error?


On 28/05/2021 17.25, Andy Seaborne wrote:



On 28/05/2021 14:59, Mikael Pesonen wrote:


I should try some older Jena/Fuseki version?


Yes.

Also
 - run on different hardware.
 - run multiple times
 - look at the data and see if anything unusual is in it.
 etc etc




On 28/05/2021 16.49, Andy Seaborne wrote:



On 28/05/2021 14:03, Mikael Pesonen wrote:


No this is the fresh db, started from empty today. And plenty of 
disk space.


So it's repeatble.

With no Minimal, Verifiable, Complete Example, it'll have to be an 
on-site investigation. Try different versions.


    Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of 
turtle, imported without warnings this time, but reading the 
graph fails with this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNext

Re: NodeTableTRDF/Read exception

2022-03-21 Thread Andy Seaborne

The only time I have seen anything similar to this is on Android where 
something other process is messing about the files. TDB is not proof 
again other processes accessing the same files, including with shared 
network drives where different computers access the same filesystem.


Andy

On 21/03/2022 11:39, Mikael Pesonen wrote:


Got this again after few days of little usage after TDB2 was rebuilt 
from empty. Would you suggest this is hw error? No possibility that its 
Jena error?


On 28/05/2021 17.25, Andy Seaborne wrote:



On 28/05/2021 14:59, Mikael Pesonen wrote:


I should try some older Jena/Fuseki version?


Yes.

Also
 - run on different hardware.
 - run multiple times
 - look at the data and see if anything unusual is in it.
 etc etc




On 28/05/2021 16.49, Andy Seaborne wrote:



On 28/05/2021 14:03, Mikael Pesonen wrote:


No this is the fresh db, started from empty today. And plenty of 
disk space.


So it's repeatble.

With no Minimal, Verifiable, Complete Example, it'll have to be an 
on-site investigation. Try different versions.


    Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of turtle, 
imported without warnings this time, but reading the graph fails 
with this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[fuseki-server.jar:3.17.0]
 at 
org.a

Re: NodeTableTRDF/Read exception

2022-03-21 Thread Mikael Pesonen




Got this again after few days of little usage after TDB2 was rebuilt 
from empty. Would you suggest this is hw error? No possibility that its 
Jena error?


On 28/05/2021 17.25, Andy Seaborne wrote:



On 28/05/2021 14:59, Mikael Pesonen wrote:


I should try some older Jena/Fuseki version?


Yes.

Also
 - run on different hardware.
 - run multiple times
 - look at the data and see if anything unusual is in it.
 etc etc




On 28/05/2021 16.49, Andy Seaborne wrote:



On 28/05/2021 14:03, Mikael Pesonen wrote:


No this is the fresh db, started from empty today. And plenty of 
disk space.


So it's repeatble.

With no Minimal, Verifiable, Complete Example, it'll have to be an 
on-site investigation. Try different versions.


    Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of turtle, 
imported without warnings this time, but reading the graph fails 
with this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply

Re: NodeTableTRDF/Read exception

2021-05-28 Thread Andy Seaborne





On 28/05/2021 14:59, Mikael Pesonen wrote:


I should try some older Jena/Fuseki version?


Yes.

Also
 - run on different hardware.
 - run multiple times
 - look at the data and see if anything unusual is in it.
 etc etc




On 28/05/2021 16.49, Andy Seaborne wrote:



On 28/05/2021 14:03, Mikael Pesonen wrote:


No this is the fresh db, started from empty today. And plenty of disk 
space.


So it's repeatble.

With no Minimal, Verifiable, Complete Example, it'll have to be an 
on-site investigation. Try different versions.


    Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of turtle, 
imported without warnings this time, but reading the graph fails 
with this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIteratorBase.hasNext(QueryIteratorBase.java:114) 
~[fuseki-server.jar

Re: NodeTableTRDF/Read exception

2021-05-28 Thread Mikael Pesonen




I should try some older Jena/Fuseki version?

On 28/05/2021 16.49, Andy Seaborne wrote:



On 28/05/2021 14:03, Mikael Pesonen wrote:


No this is the fresh db, started from empty today. And plenty of disk 
space.


So it's repeatble.

With no Minimal, Verifiable, Complete Example, it'll have to be an 
on-site investigation. Try different versions.


    Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of turtle, 
imported without warnings this time, but reading the graph fails 
with this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.j

Re: NodeTableTRDF/Read exception

2021-05-28 Thread Andy Seaborne





On 28/05/2021 14:03, Mikael Pesonen wrote:


No this is the fresh db, started from empty today. And plenty of disk 
space.


So it's repeatble.

With no Minimal, Verifiable, Complete Example, it'll have to be an 
on-site investigation. Try different versions.


Andy



On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of turtle, 
imported without warnings this time, but reading the graph fails with 
this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~

Re: NodeTableTRDF/Read exception

2021-05-28 Thread Mikael Pesonen




No this is the fresh db, started from empty today. And plenty of disk space.

On 28/05/2021 15.58, Andy Seaborne wrote:

Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of turtle, 
imported without warnings this time, but reading the graph fails with 
this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
 at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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

Re: NodeTableTRDF/Read exception

2021-05-28 Thread Andy Seaborne


Why are you adding data to a broken database?

On 28/05/2021 12:02, Mikael Pesonen wrote:


Actually now it happened again. Same size, about 80MB of turtle, 
imported without warnings this time, but reading the graph fails with 
this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
     at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
     at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
     at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
     at

Re: NodeTableTRDF/Read exception

2021-05-28 Thread Mikael Pesonen




Actually now it happened again. Same size, about 80MB of turtle, 
imported without warnings this time, but reading the graph fails with 
this exception.


13:59:39 WARN  Fuseki  :: [44] 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:113) 
~[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-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.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.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.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
    at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
    at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
    at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[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.QueryIterRepeatApply.makeNextStage(QueryIterRepeatApply.java:101) 
~[fuseki-server.jar:3.17.0]
    at 
org.apache.jena.sparql.engine.iterator.QueryIterRepeatApply.hasNextBinding(QueryIterRepeatApply.java:65) 
~[fuseki-server.ja

Re: NodeTableTRDF/Read exception

2021-05-27 Thread Andy Seaborne

See the thread following from Harri's message "TDBException: 
NodeTableTRDF/Read (vol. 2)"


Andy


On 27/05/2021 15:56, Mikael Pesonen wrote:


Tried with the invalid data on fresh db and it didn't cause this 
exception. So root cause happened probably way earlier and is unknown.


On 20/05/2021 14.10, Andy Seaborne wrote:

Please can we have a complete, minimal example.

On 19/05/2021 11:12, Mikael Pesonen wrote:


More info on this. When the causes of the two warnings are fixed, 
same data is imported correctly and everything works.
So, when there are "too many" WARN level errors in importing data, 
the graph becomes corrupted.


Unlikely to be related to how many.

You wrote:
>> but many warnings on invalid data

not two.  What is the problem data?

    Andy


On 18/05/2021 18.02, Andy Seaborne wrote:



On 18/05/2021 13:03, Mikael Pesonen wrote:


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: 
 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

...



Most likely different issues - these are to do with your data (being 
read in?).


They don't appear related but you could try a minimal test case 
based on that data.


Another thing to investigate is to look at the earlier log entries 
for [24] and see if you can spot the RDF terms that are affected by 
comparing them to other incidents.


Maybe it is just one entry in the node table, or maybe not.

    Andy


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.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 


...
Caused by: org.apache.thrift.protocol.TProtocolException: 
Unrecognized type 0
 at 
org.apache.thrift.protoc

Re: NodeTableTRDF/Read exception

2021-05-27 Thread Mikael Pesonen




Tried with the invalid data on fresh db and it didn't cause this 
exception. So root cause happened probably way earlier and is unknown.


On 20/05/2021 14.10, Andy Seaborne wrote:

Please can we have a complete, minimal example.

On 19/05/2021 11:12, Mikael Pesonen wrote:


More info on this. When the causes of the two warnings are fixed, 
same data is imported correctly and everything works.
So, when there are "too many" WARN level errors in importing data, 
the graph becomes corrupted.


Unlikely to be related to how many.

You wrote:
>> but many warnings on invalid data

not two.  What is the problem data?

    Andy


On 18/05/2021 18.02, Andy Seaborne wrote:



On 18/05/2021 13:03, Mikael Pesonen wrote:


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: 
 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

...



Most likely different issues - these are to do with your data (being 
read in?).


They don't appear related but you could try a minimal test case 
based on that data.


Another thing to investigate is to look at the earlier log entries 
for [24] and see if you can spot the RDF terms that are affected by 
comparing them to other incidents.


Maybe it is just one entry in the node table, or maybe not.

    Andy


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.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 


...
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(TProtocolUti

Re: NodeTableTRDF/Read exception

2021-05-21 Thread Mikael Pesonen




Unfortunately the data is confidential. I can try to generate the same 
errors on reseted db if same thing happens.


On 20/05/2021 14.10, Andy Seaborne wrote:

Please can we have a complete, minimal example.

On 19/05/2021 11:12, Mikael Pesonen wrote:


More info on this. When the causes of the two warnings are fixed, 
same data is imported correctly and everything works.
So, when there are "too many" WARN level errors in importing data, 
the graph becomes corrupted.


Unlikely to be related to how many.

You wrote:
>> but many warnings on invalid data

not two.  What is the problem data?

    Andy


On 18/05/2021 18.02, Andy Seaborne wrote:



On 18/05/2021 13:03, Mikael Pesonen wrote:


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: 
 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

...



Most likely different issues - these are to do with your data (being 
read in?).


They don't appear related but you could try a minimal test case 
based on that data.


Another thing to investigate is to look at the earlier log entries 
for [24] and see if you can spot the RDF terms that are affected by 
comparing them to other incidents.


Maybe it is just one entry in the node table, or maybe not.

    Andy


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.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 


...
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-

Re: NodeTableTRDF/Read exception

2021-05-20 Thread Andy Seaborne


Please can we have a complete, minimal example.

On 19/05/2021 11:12, Mikael Pesonen wrote:


More info on this. When the causes of the two warnings are fixed, same 
data is imported correctly and everything works.
So, when there are "too many" WARN level errors in importing data, the 
graph becomes corrupted.


Unlikely to be related to how many.

You wrote:
>> but many warnings on invalid data

not two.  What is the problem data?

Andy


On 18/05/2021 18.02, Andy Seaborne wrote:



On 18/05/2021 13:03, Mikael Pesonen wrote:


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: 
 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

...



Most likely different issues - these are to do with your data (being 
read in?).


They don't appear related but you could try a minimal test case based 
on that data.


Another thing to investigate is to look at the earlier log entries for 
[24] and see if you can spot the RDF terms that are affected by 
comparing them to other incidents.


Maybe it is just one entry in the node table, or maybe not.

    Andy


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.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 


...
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

Re: NodeTableTRDF/Read exception

2021-05-19 Thread Mikael Pesonen




More info on this. When the causes of the two warnings are fixed, same 
data is imported correctly and everything works.
So, when there are "too many" WARN level errors in importing data, the 
graph becomes corrupted.


On 18/05/2021 18.02, Andy Seaborne wrote:



On 18/05/2021 13:03, Mikael Pesonen wrote:


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: 
 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

...



Most likely different issues - these are to do with your data (being 
read in?).


They don't appear related but you could try a minimal test case based 
on that data.


Another thing to investigate is to look at the earlier log entries for 
[24] and see if you can spot the RDF terms that are affected by 
comparing them to other incidents.


Maybe it is just one entry in the node table, or maybe not.

    Andy


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.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 


...
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

Re: NodeTableTRDF/Read exception

2021-05-19 Thread Mikael Pesonen




This error occurs with all actions related to same graph. So I can't for 
example drop or clear the graph anymore.

Actions on other graphs work as usual.

On 18/05/2021 18.02, Andy Seaborne wrote:



On 18/05/2021 13:03, Mikael Pesonen wrote:


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: 
 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

...



Most likely different issues - these are to do with your data (being 
read in?).


They don't appear related but you could try a minimal test case based 
on that data.


Another thing to investigate is to look at the earlier log entries for 
[24] and see if you can spot the RDF terms that are affected by 
comparing them to other incidents.


Maybe it is just one entry in the node table, or maybe not.

    Andy


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.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 


...
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]

Re: NodeTableTRDF/Read exception

2021-05-18 Thread Andy Seaborne





On 18/05/2021 13:03, Mikael Pesonen wrote:


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: 
 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

...



Most likely different issues - these are to do with your data (being 
read in?).


They don't appear related but you could try a minimal test case based on 
that data.


Another thing to investigate is to look at the earlier log entries for 
[24] and see if you can spot the RDF terms that are affected by 
comparing them to other incidents.


Maybe it is just one entry in the node table, or maybe not.

Andy


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.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 


...
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 Serve

Re: NodeTableTRDF/Read exception

2021-05-18 Thread Mikael Pesonen




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: 
 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]

Re: NodeTableTRDF/Read exception

2021-04-27 Thread Mikael Pesonen




Server just ran out of disk space, but it's since been on low usage so 
could have happened few months ago. And logs are only for 1 month...


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

Speech Applications - Language Management - Translation - Reader's and Writer's 
Tools - Text Tools - E-books and M-books

Mikael Pesonen
System Engineer

e-mail: mikael.peso...@lingsoft.fi
Tel. +358 2 279 3300

Time zone: GMT+2

Helsinki Office
Eteläranta 10
FI-00130 Helsinki
FINLAND

Turku Office
Kauppiaskatu 5 A
FI-20100 Turku
FINLAND

Re: NodeTableTRDF/Read exception

2021-04-27 Thread Andy Seaborne





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

Re: NodeTableTRDF/Read exception

2021-04-27 Thread Mikael Pesonen




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?


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

Speech Applications - Language Management - Translation - Reader's and Writer's 
Tools - Text Tools - E-books and M-books

Mikael Pesonen
System Engineer

e-mail: mikael.peso...@lingsoft.fi
Tel. +358 2 279 3300

Time zone: GMT+2

Helsinki Office
Eteläranta 10
FI-00130 Helsinki
FINLAND

Turku Office
Kauppiaskatu 5 A
FI-20100 Turku
FINLAND

Re: NodeTableTRDF/Read exception

2021-04-27 Thread Andy Seaborne


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

Re: NodeTableTRDF/Read exception

2021-04-26 Thread Mikael Pesonen




Found this too, then nothing else for last month in journalctl

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]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.dboe.base.buffer.RecordBuffer.find(RecordBuffer.java:167) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.dboe.base.buffer.RecordBuffer.find(RecordBuffer.java:124) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.dboe.trans.bplustree.BPTreeRecords.internalInsert(BPTreeRecords.java:158) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.dboe.trans.bplustree.BPTreeNode.internalInsert(BPTreeNode.java:522) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.dboe.trans.bplustree.BPTreeNode.internalInsert(BPTreeNode.java:522) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.dboe.trans.bplustree.BPTreeNode.insert(BPTreeNode.java:203) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.dboe.trans.bplustree.BPlusTree.insertAndReturnOld(BPlusTree.java:278) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.dboe.trans.bplustree.BPlusTree.insert(BPlusTree.java:271) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.tdb2.store.tupletable.TupleIndexRecord.performAdd(TupleIndexRecord.java:94) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.tdb2.store.tupletable.TupleIndexBase.add(TupleIndexBase.java:66) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.tdb2.store.tupletable.TupleTable.add(TupleTable.java:95) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.tdb2.store.nodetupletable.NodeTupleTableConcrete.addRow(NodeTupleTableConcrete.java:79) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.tdb2.store.QuadTable.add(QuadTable.java:57) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.tdb2.store.StorageTDB.add(StorageTDB.java:117) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.dboe.storage.system.DatasetGraphStorage.add(DatasetGraphStorage.java:165) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.sparql.core.DatasetGraphWrapper.add(DatasetGraphWrapper.java:176) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.sparql.core.DatasetGraphWrapper.add(DatasetGraphWrapper.java:176) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.sparql.core.DatasetGraphMonitor.add$(DatasetGraphMonitor.java:115) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.sparql.core.DatasetGraphMonitor.add(DatasetGraphMonitor.java:110) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.sparql.core.GraphView.performAdd(GraphView.java:152) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.graph.impl.GraphBase.add(GraphBase.java:184) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.riot.system.StreamRDFLib$ParserOutputGraph.triple(StreamRDFLib.java:181) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.riot.system.StreamRDFWrapper.triple(StreamRDFWrapper.java:40) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.riot.system.StreamRDFCountingBase.triple(StreamRDFCountingBase.java:39) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.riot.system.StreamRDFWrapper.triple(StreamRDFWrapper.java:40) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.riot.system.StreamRDFCountingBase.triple(StreamRDFCountingBase.java:39) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.riot.lang.LangTurtle.emit(LangTurtle.java:57) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.riot.lang.LangTurtleBase.emitTriple(LangTurtleBase.java:561) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.riot.lang.LangTurtleBase.objectList(LangTurtleBase.java:424) 
~[fuseki-server.jar:3.17.0]
Apr 12 12:30:55 solid java[22910]: at 
org.apache.jena.riot.lang.LangTurtleBase.predicateObject

Re: NodeTableTRDF/Read exception

2021-04-26 Thread Mikael Pesonen




There are few of these too (I'm grepping journalctl with 'fuseki'):

Mar 22 16:04:22 solid java[1398]: [2021-03-22 16:04:22] WebAppContext 
WARN  Failed startup of context o.e.j.w.WebAppContext@15dd5ac2{Apache 
Jena Fuseki Server,/,file:///opt/insight/jena/webapp/,UNAVAILABLE}
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:165) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.open(AssemblerGroup.java:144) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.assembler.assemblers.AssemblerGroup$ExpandingAssemblerGroup.open(AssemblerGroup.java:93) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:39) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:35) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.fuseki.build.FusekiConfig.getDataset(FusekiConfig.java:687) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.fuseki.build.FusekiConfig.buildDataService(FusekiConfig.java:444) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.fuseki.build.FusekiConfig.buildDataAccessPoint(FusekiConfig.java:434) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.fuseki.webapp.FusekiWebapp.configFromTemplate(FusekiWebapp.java:323) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.fuseki.webapp.FusekiWebapp.initServerConfiguration(FusekiWebapp.java:252) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.fuseki.webapp.FusekiWebapp.initializeDataAccessPoints(FusekiWebapp.java:219) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.fuseki.webapp.FusekiServerListener.serverInitialization(FusekiServerListener.java:97) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.apache.jena.fuseki.webapp.FusekiServerListener.contextInitialized(FusekiServerListener.java:57) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.server.handler.ContextHandler.callContextInitialized(ContextHandler.java:1068) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.servlet.ServletContextHandler.callContextInitialized(ServletContextHandler.java:572) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.server.handler.ContextHandler.contextInitialized(ContextHandler.java:997) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.servlet.ServletHandler.initialize(ServletHandler.java:746) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.servlet.ServletContextHandler.startContext(ServletContextHandler.java:379) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.webapp.WebAppContext.startWebapp(WebAppContext.java:1457) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1422) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.server.handler.ContextHandler.doStart(ContextHandler.java:911) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.servlet.ServletContextHandler.doStart(ServletContextHandler.java:288) 
~[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:524) 
[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:73) 
[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:169) 
[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:110) 
[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:97) 
[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.server.handler.gzip.GzipHandler.doStart(GzipHandler.java:426) 
[fuseki-server.jar:3.17.0]
Mar 22 16:04:22 solid java[1398]: at 
org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:73) 
[fuseki-server.jar:3.

Re: NodeTableTRDF/Read exception

2021-04-26 Thread Andy Seaborne




On 26/04/2021 10:19, Mikael Pesonen wrote:


Is this correct one:


Well, it's not the one you showed in the initial message which was

Apr 23 13:51:09 solid java[6846]: [2021-04-23 13:51:09] Fuseki WARN  [2] 
RC = 500 : NodeTableTRDF/Read


but the important question is:

Do you have the logs from when the update/disk full incident happened?

That seems like it is when the problem started. The rest are consequences.

Andy



Apr 23 14:34:58 solid java[1153]: [2021-04-23 14:34:58] Fuseki INFO  [1] 
500 Server Error (1.976 s)
Apr 23 15:30:27 solid systemd[1]: Configuration file 
/lib/systemd/system/apache-jena-fuseki.service is marked 
world-inaccessible. This has no effect as configuration data is 
accessible via APIs without restrictions. Proceeding anyway.
Apr 23 15:30:27 solid systemd[1]: Configuration file 
/lib/systemd/system/apache-jena-fuseki.path is marked 
world-inaccessible. This has no effect as configuration data is 
accessible via APIs without restrictions. Proceeding anyway.
Apr 23 15:30:34 solid systemd[1]: Configuration file 
/lib/systemd/system/apache-jena-fuseki.service is marked 
world-inaccessible. This has no effect as configuration data is 
accessible via APIs without restrictions. Proceeding anyway.
Apr 23 15:30:54 solid sudo[21457]:   **: TTY=pts/0 ; PWD=/home/**; 
USER=root ; COMMAND=/bin/cat /lib/systemd/system/apache-jena-fuseki.service
Apr 23 15:31:44 solid sudo[22157]:   **: TTY=pts/1 ; PWD=/home/**; 
USER=root ; COMMAND=/bin/cat /lib/systemd/system/apache-jena-fuseki.service


After that comes NodeTableTRDF/Read exception.



On 23/04/2021 21.11, Andy Seaborne wrote:



On 23/04/2021 14:57, Mikael Pesonen wrote:


Sorry here is the entire log


It's a different log. [2] is now [5]



Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO 
[5] POST http://nimisampo.lingsoft.fi:3030/ds
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO 
[6] POST http://nimisampo.lingsoft.fi:3030/ds
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [5] 


Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO 
[6] 200 OK (155 ms)



Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki WARN 
[5] RC = 500 : NodeTableTRDF/Read
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) 
~[fuseki-server.jar:3.17.0]

...

~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:135) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:773) 
[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:905) 
[fuseki-server.jar:3.17.0]


This seems to be two stacktraces or printing the "caused by" seems to 
be wrong


TProtocolUtil:144 is an exception throw.

Regardless, the node table is broken.

Do you have the logs from when the update/disk full incident happened?

   Andy


Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:144) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:60) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:433) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.TUnion.read(TUnion.java:138) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:82) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO 
[5] 500 Server Error (568 ms)



On 23/04/2021 16.40, Andy Seaborne wrote:



On 23/04/2021 13:33, Mikael Pesonen wrote:


Hi,

we get this exception now when starting Jena and it's not loading 
any data. I have no idea what is changed on the server.


Apr 23 13:51:09 solid java[6846]: [2021-04-23 13:51:09] Fuseki WARN 
[2] RC = 500 : NodeTableTRDF/Read
Apr 23 13:51:09 solid java[6846]: 
org.apache.jena.tdb2.TDBException: NodeTableTRDF/Read
Apr 23 13:51:09 solid java[6846]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) 
~[fuseki-server.jar:3.17.0]
Apr 23 13:51:09 solid java[6846]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTa

Re: NodeTableTRDF/Read exception

2021-04-26 Thread Mikael Pesonen




Is this correct one:

Apr 23 14:34:58 solid java[1153]: [2021-04-23 14:34:58] Fuseki INFO  [1] 
500 Server Error (1.976 s)
Apr 23 15:30:27 solid systemd[1]: Configuration file 
/lib/systemd/system/apache-jena-fuseki.service is marked 
world-inaccessible. This has no effect as configuration data is 
accessible via APIs without restrictions. Proceeding anyway.
Apr 23 15:30:27 solid systemd[1]: Configuration file 
/lib/systemd/system/apache-jena-fuseki.path is marked 
world-inaccessible. This has no effect as configuration data is 
accessible via APIs without restrictions. Proceeding anyway.
Apr 23 15:30:34 solid systemd[1]: Configuration file 
/lib/systemd/system/apache-jena-fuseki.service is marked 
world-inaccessible. This has no effect as configuration data is 
accessible via APIs without restrictions. Proceeding anyway.
Apr 23 15:30:54 solid sudo[21457]:   **: TTY=pts/0 ; PWD=/home/**; 
USER=root ; COMMAND=/bin/cat /lib/systemd/system/apache-jena-fuseki.service
Apr 23 15:31:44 solid sudo[22157]:   **: TTY=pts/1 ; PWD=/home/**; 
USER=root ; COMMAND=/bin/cat /lib/systemd/system/apache-jena-fuseki.service


After that comes NodeTableTRDF/Read exception.



On 23/04/2021 21.11, Andy Seaborne wrote:



On 23/04/2021 14:57, Mikael Pesonen wrote:


Sorry here is the entire log


It's a different log. [2] is now [5]



Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  
[5] POST http://nimisampo.lingsoft.fi:3030/ds
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  
[6] POST http://nimisampo.lingsoft.fi:3030/ds
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [5] 


Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  
[6] 200 OK (155 ms)



Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki WARN  
[5] RC = 500 : NodeTableTRDF/Read
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) 
~[fuseki-server.jar:3.17.0]

...

~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:135) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:773) 
[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:905) 
[fuseki-server.jar:3.17.0]


This seems to be two stacktraces or printing the "caused by" seems to 
be wrong


TProtocolUtil:144 is an exception throw.

Regardless, the node table is broken.

Do you have the logs from when the update/disk full incident happened?

   Andy


Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:144) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:60) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:433) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.TUnion.read(TUnion.java:138) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:82) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  
[5] 500 Server Error (568 ms)



On 23/04/2021 16.40, Andy Seaborne wrote:



On 23/04/2021 13:33, Mikael Pesonen wrote:


Hi,

we get this exception now when starting Jena and it's not loading 
any data. I have no idea what is changed on the server.


Apr 23 13:51:09 solid java[6846]: [2021-04-23 13:51:09] Fuseki WARN 
[2] RC = 500 : NodeTableTRDF/Read
Apr 23 13:51:09 solid java[6846]: 
org.apache.jena.tdb2.TDBException: NodeTableTRDF/Read
Apr 23 13:51:09 solid java[6846]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) 
~[fuseki-server.jar:3.17.0]
Apr 23 13:51:09 solid java[6846]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103) 
~[fuseki-server.jar:3.17.0]


TDBException wraps a Thrift exception which has the details.



Any idea what is going on? There was shortage of disk space, hope 
the db is not corrupted.


You would have got errors at update time.

   Andy





Service:

ExecStart=/usr/lib/jvm/java-8-oracle/bin/java -Xmx3000M -jar 
/opt/insight/jena/fuseki-server.jar --update --port 3030 
--config=/op

Re: NodeTableTRDF/Read exception

2021-04-23 Thread Andy Seaborne





On 23/04/2021 14:57, Mikael Pesonen wrote:


Sorry here is the entire log


It's a different log. [2] is now [5]



Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [5] 
POST http://nimisampo.lingsoft.fi:3030/ds
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [6] 
POST http://nimisampo.lingsoft.fi:3030/ds
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [5] 


Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [6] 
200 OK (155 ms)



Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki WARN  [5] 
RC = 500 : NodeTableTRDF/Read
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) 
~[fuseki-server.jar:3.17.0]

...

~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:135) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:773) 
[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:905) 
[fuseki-server.jar:3.17.0]


This seems to be two stacktraces or printing the "caused by" seems to be 
wrong


TProtocolUtil:144 is an exception throw.

Regardless, the node table is broken.

Do you have the logs from when the update/disk full incident happened?

Andy


Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:144) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.protocol.TProtocolUtil.skip(TProtocolUtil.java:60) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:433) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.thrift.TUnion.read(TUnion.java:138) ~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:82) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [5] 
500 Server Error (568 ms)



On 23/04/2021 16.40, Andy Seaborne wrote:



On 23/04/2021 13:33, Mikael Pesonen wrote:


Hi,

we get this exception now when starting Jena and it's not loading any 
data. I have no idea what is changed on the server.


Apr 23 13:51:09 solid java[6846]: [2021-04-23 13:51:09] Fuseki WARN 
[2] RC = 500 : NodeTableTRDF/Read
Apr 23 13:51:09 solid java[6846]: org.apache.jena.tdb2.TDBException: 
NodeTableTRDF/Read
Apr 23 13:51:09 solid java[6846]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) 
~[fuseki-server.jar:3.17.0]
Apr 23 13:51:09 solid java[6846]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103) 
~[fuseki-server.jar:3.17.0]


TDBException wraps a Thrift exception which has the details.



Any idea what is going on? There was shortage of disk space, hope the 
db is not corrupted.


You would have got errors at update time.

   Andy





Service:

ExecStart=/usr/lib/jvm/java-8-oracle/bin/java -Xmx3000M -jar 
/opt/insight/jena/fuseki-server.jar --update --port 3030 
--config=/opt/insight/jena/run/fuseki_config.ttl


Config:

PREFIX : <#>
PREFIX fuseki: 
PREFIX rdf: 
PREFIX rdfs: 
PREFIX ja: 

PREFIX tdb2: 
PREFIX text: 

PREFIX lsrm: 

[] rdf:type fuseki:Server ;
fuseki:services (
:service
) .

:service rdf:type fuseki:Service ;
fuseki:name "/ds" ; # http://host:port/ds-ro
fuseki:serviceQuery "query" ; # SPARQL query service
fuseki:serviceQuery "sparql" ; # SPARQL query service
fuseki:serviceUpdate "update" ; # SPARQL update service
fuseki:serviceUpload "upload" ; # Non-SPARQL upload service
fuseki:serviceReadWriteGraphStore "data" ; # SPARQL Graph store 
protocol (read and write)

fuseki:dataset :text_dataset ;
.

:text_dataset rdf:type text:TextDataset ;
text:dataset :tdb2_dataset ;
text:index :indexLucene ;
.
:tdb2_dataset rdf:type tdb2:DatasetTDB2 ;
tdb2:location "/opt/insight/jena_data/" ;
.

# Text index description
:indexLucene a text:TextIndexLucene ;
text:directory  ;
text:entityMap :entMap

Re: NodeTableTRDF/Read exception

2021-04-23 Thread Mikael Pesonen




Sorry here is the entire log

Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [5] 
POST http://nimisampo.lingsoft.fi:3030/ds
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [6] 
POST http://nimisampo.lingsoft.fi:3030/ds
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [5] 
Query =    PREFIX text:    PREFIX 
rdfs:    PREFIX rdf: 
   PREFIX xsd: 
   PREFIX vcard: 
   PREFIX foaf: 
   PREFIX dc: 
   PREFIX dcterms: 
   PREFIX dcat: 
   PREFIX skos: 
   PREFIX org: 
   PREFIX lifecycle: 
   PREFIX lsrm: 
 SELECT *   FROM 
 FROM 
 
WHERE { ?s a foaf:Person . ?s 
vcard:fn ?prefLabel . ?s vcard:family-name ?familyNameLabel 
. OPTIONAL {  ?s vcard:given-name ?givenNameLabel . 
}OPTIONAL {  ?s skos:altLabel ?altNameLabel .  }OPTIONAL 
{  ?s vcard:hasTelephone ?phone . ?phone a vcard:Voice 
. ?phone rdfs:label ?phoneLabel . OPTIONAL {   ?phone 
rdf:type lsrm:Preferred  . BIND (?phone AS ?prefPhone) }  
}OPTIONAL {  ?s vcard:hasEmail ?email . ?email 
rdfs:label ?emailLabel . OPTIONAL {   ?email rdf:type 
lsrm:Preferred .   BIND (?email AS ?prefEmail) 
}  }OPTIONAL {  ?s vcard:hasInstantMessage ?skype 
. ?skype a vcard:Voice . ?skype vcard:hasValue ?svalue . 
FILTER (regex(str(?svalue), "skype:")) ?skype rdfs:label 
?skypeLabel .  OPTIONAL {   ?skype rdf:type 
lsrm:Preferred  .   BIND (?skype AS ?prefSkype) }    
}OPTIONAL {  ?s org:memberOf ?group . ?group 
skos:prefLabel ?groupL
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [6] 
Query =    PREFIX text:    PREFIX 
rdfs:    PREFIX rdf: 
   PREFIX xsd: 
   PREFIX vcard: 
   PREFIX foaf: 
   PREFIX dc: 
   PREFIX dcterms: 
   PREFIX dcat: 
   PREFIX skos: 
   PREFIX org: 
   PREFIX lifecycle: 
   PREFIX lsrm: 
 SELECT DISTINCT *   
FROM 
 
FROM  WHERE 
{   {  {   ?s skos:broader* 
 
.   ?s skos:narrower ?o .   ?s skos:prefLabel ?sLabel 
.   FILTER NOT EXISTS {  ?s skos:prefLabel ?sLabel2 
. FILTER(?sLabel != ?sLabel2) . 
FILTER(lang(?sLabel2) = 'fi') . }   ?o skos:prefLabel ?oLabel 
.   FILTER NOT EXISTS {  ?o skos:prefLabel ?oLabel2 
. FILTER(?oLabel != ?oLabel2) . FILTER(lang(?oLabel2) = 
'fi') .   } BIND ('title' AS 
?field) .   OPTIONAL {   VALUES ?s 
{} 
.   BIND (true AS ?root) 
.   }  }  }UNION{ {   ?s 
skos:broader* 
 
.   ?s skos:narrower ?o .   ?s skos:prefLabel ?sLabel 
.   FILTER NOT EXISTS {  ?s skos:prefLabel ?sLabel2 .
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki INFO  [6] 
200 OK (155 ms)
Apr 23 16:23:49 solid java[1153]: [2021-04-23 16:23:49] Fuseki WARN  [5] 
RC = 500 : NodeTableTRDF/Read
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) 
~[fuseki-server.jar:3.17.0]
Apr 23 16:23:49 solid java[1153]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103) 
~[fuseki-server.jar:3.17.0

Re: NodeTableTRDF/Read exception

2021-04-23 Thread Andy Seaborne





On 23/04/2021 13:33, Mikael Pesonen wrote:


Hi,

we get this exception now when starting Jena and it's not loading any 
data. I have no idea what is changed on the server.


Apr 23 13:51:09 solid java[6846]: [2021-04-23 13:51:09] Fuseki WARN  [2] 
RC = 500 : NodeTableTRDF/Read
Apr 23 13:51:09 solid java[6846]: org.apache.jena.tdb2.TDBException: 
NodeTableTRDF/Read
Apr 23 13:51:09 solid java[6846]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:87) 
~[fuseki-server.jar:3.17.0]
Apr 23 13:51:09 solid java[6846]: at 
org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103) 
~[fuseki-server.jar:3.17.0]


TDBException wraps a Thrift exception which has the details.



Any idea what is going on? There was shortage of disk space, hope the db 
is not corrupted.


You would have got errors at update time.

Andy





Service:

ExecStart=/usr/lib/jvm/java-8-oracle/bin/java -Xmx3000M -jar 
/opt/insight/jena/fuseki-server.jar --update --port 3030 
--config=/opt/insight/jena/run/fuseki_config.ttl


Config:

PREFIX : <#>
PREFIX fuseki: 
PREFIX rdf: 
PREFIX rdfs: 
PREFIX ja: 

PREFIX tdb2: 
PREFIX text: 

PREFIX lsrm: 

[] rdf:type fuseki:Server ;
fuseki:services (
:service
) .

:service rdf:type fuseki:Service ;
fuseki:name "/ds" ; # http://host:port/ds-ro
fuseki:serviceQuery "query" ; # SPARQL query service
fuseki:serviceQuery "sparql" ; # SPARQL query service
fuseki:serviceUpdate "update" ; # SPARQL update service
fuseki:serviceUpload "upload" ; # Non-SPARQL upload service
fuseki:serviceReadWriteGraphStore "data" ; # SPARQL Graph store protocol 
(read and write)

fuseki:dataset :text_dataset ;
.

:text_dataset rdf:type text:TextDataset ;
text:dataset :tdb2_dataset ;
text:index :indexLucene ;
.
:tdb2_dataset rdf:type tdb2:DatasetTDB2 ;
tdb2:location "/opt/insight/jena_data/" ;
.

# Text index description
:indexLucene a text:TextIndexLucene ;
text:directory  ;
text:entityMap :entMap ;
text:storeValues true ;
#text:analyzer [ a text:StandardAnalyzer ] ;
#text:queryAnalyzer [ a text:KeywordAnalyzer ] ;
#text:queryParser text:QueryParser ; # text:AnalyzingQueryParser
#text:multilingualSupport true ;
.

:entMap a text:EntityMap ;
text:entityField "uri" ;
## Must be defined in the text:map
text:defaultField "lsrm_lmz_title" ;
## Enable deleting of text index entries.
text:uidField "uid" ;
text:langField "lang" ;
text:graphField "graph" ;
text:map (
[ text:field "lsrm_lmz_title" ; text:predicate lsrm:lmz_title]
[ text:field "lsrm_lmz_content" ; text:predicate lsrm:lmz_content]
)
.

Re: NodeTableTRDF/Read exception

Re: NodeTableTRDF/Read exception

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