Hi Guil, if you run inferences over a SPIN model, then these inferences may interfere with the RDF syntax of the SPARQL queries, and the string serialization may fail. Similarly, it's possible to mess up the triples of an OWL structure through inferences. Make sure to leave the SPIN rules in a separate graph that is outside of the inference query model.
(Just a wild guess at what's going on). Cheers, Holger On Nov 18, 2011, at 8:40 PM, Guilherme Scomparim wrote: > Hi Scott, > > Thanks for the information. You are right, the problem is something on my > code. > > I have a model that when I run Jena and Top SPIN inferences I get the > following error > > Malformed resource: Labels plugin > org.topbraid.spintb.labels.SPINExpressionsLabelsPlugin@5d258f31 could not > render 5b90bc16:133b62bef3a:-1bfe > java.lang.StackOverflowError > > This same model I use in my save and open SPARQLMotion script where I > import the model and then run the inferences on it. The funny thing is that > when I run the script I do not get any error, it just takes for ever on the > jena inference step on the first time I run it, but after it looked it was > working ok. > > I am trying to understand what in the file is giving me error, but it does > not really make any sense. Does this message tells something I should look > for? > > This is just happening on 352 the same model works fine in 340. > > Thanks again, > Guil > > Guil Scomparim > +61413997827 > > > > Date: Thu, 17 Nov 2011 08:01:44 -0800 > > Subject: [topbraid-users] Re: Error when opening some classes in TDB files > > From: [email protected] > > To: [email protected] > > > > Guil; It appears you code has some problems writing to TDB. This > > isn't an issue we can help much on. The Jena forum may have some tips > > for you. > > > > Multiple concurrent commits to <urn:x-tb:session> are fully supported > > by EVN and Ensemble. <urn:x-tb:session> is a graph designed for > > representing session data in those applications alone. It is not > > supported for use in other applications. > > > > -- Scott > > > > On Nov 16, 10:13 pm, "Guilherme Scomparim" <[email protected]> > > wrote: > > > Hi Scott, > > > > > > Thank you for the quick reply. > > > > > > Here are the steps before I got the problem. > > > 1) The TDB file was created by using the export functionality from a owl > > > file a week ago. > > > 2) I then Set up the teamwork changes repository > > > 3) I have been updating it with my framework that works like EVN where > > > instead of using SKOS I have an ontology that captures some meta-data and > > > perform some inferences. > > > 4) Yesterday I was already getting some errors (null exceptions) when > > > opening the file, but with some work around, the file would open ok > > > 5) Today after some more investigation I realised that the error occur > > > only on files that I changed yesterday. The sequence to simulate the error > > > is by selecting any class (That I included instances yesterday) in the > > > class > > > view when the "instance tab" is the focus or is selected. > > > 6) Later I could not even open properly some of the files. It seams that > > > the tdb files got corrupted, because if I try to export the models I still > > > can open I get the same error. > > > > > > I am even started from the scratch using my models from the backup > > > before > > > yesterday changes. But I would like to understand what I done wrong > > > > > > The only thing I can think that I done different yesterday is that I did > > > open all the corrupted models at the same time in different tabs of the > > > browser, where I performed many scripts that have functions that > > > manipulate > > > the <urn:x-tb:session> graph and commit changes simultaneously in > > > different > > > models. Do you think this could be the problem? > > > > > > I hope this helps, Thanks again > > > Guil > > > > > > -----Original Message----- > > > From: Scott Henninger > > > Sent: Thursday, November 17, 2011 1:08 PM > > > To: TopBraid Suite Users > > > Subject: [topbraid-users] Re: Error when opening some classes in TDB files > > > > > > Darn, the opening sentence should be "Can you provide some information > > > on how the TDB files and file connector were created?", where the file > > > connector is the .tdb file. > > > > > > -- Scott > > > > > > On Nov 16, 8:06 pm, Scott Henninger <[email protected]> > > > wrote: > > > > Guil; Can you provide some information on how the RDB files and file > > > > connector were created? You say when you select "some classes", so > > > > what are the characteristics of those class definitions that could be > > > > different than others? For example, if you also have the Instances > > > > view open, then Composer will try to cache some class instances. The > > > > problem appears to occur when Composer tries to populate the Instances > > > > view. So that could explain why it happens "some" time, the "some" > > > > being when the Instances view is open and the class has instances, and > > > > also indicates problems with instances in the TDB data store. > > > > Otherwise, we'd need more information on the context of the error to > > > > speculate further... > > > > > > > -- Scott > > > > > > > On Nov 16, 4:40 pm, Guilherme Scomparim <[email protected]> > > > > wrote: > > > > > > > > Hi all, > > > > > > > > When I open some of my TDB files in Composer and on the class view I > > > > > select some classes I get the error below. > > > > > > > > Any ideas on how to fix it? > > > > > > > > Regards, > > > > > Guil > > > > > > > > Operation failed. > > > > > On: 17/11/2011 9:35:06 AM > > > > > Reason: > > > > > java.util.NoSuchElementException > > > > > at > > > > > org.openjena.riot.tokens.TokenizerText.next(TokenizerText.java:91) > > > > > at > > > > > com.hp.hpl.jena.tdb.nodetable.NodecSSE.decode(NodecSSE.java:100) > > > > > at com.hp.hpl.jena.tdb.lib.NodeLib.decode(NodeLib.java:85) > > > > > at > > > > > com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:67) > > > > > at > > > > > com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeByNodeId(NodeTableNative.java: > > > > > 158) > > > > > at > > > > > com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java: > > > > > 85) > > > > > at > > > > > com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java: > > > > > 58) > > > > > at > > > > > com.hp.hpl.jena.tdb.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java: > > > > > 86) > > > > > at > > > > > com.hp.hpl.jena.tdb.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java: > > > > > 57) > > > > > at > > > > > com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java: > > > > > 43) > > > > > at > > > > > com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java: > > > > > 55) > > > > > at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:108) > > > > > at com.hp.hpl.jena.tdb.lib.TupleLib.triple(TupleLib.java:103) > > > > > at > > > > > com.hp.hpl.jena.tdb.lib.TupleLib.access$000(TupleLib.java:32) > > > > > at > > > > > com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:64) > > > > > at > > > > > com.hp.hpl.jena.tdb.lib.TupleLib$3.convert(TupleLib.java:60) > > > > > at org.openjena.atlas.iterator.Iter$4.next(Iter.java:265) > > > > > at com.hp.hpl.jena.tdb.store.GraphTDBBase > > > > > $MapperIteratorTriples.next(GraphTDBBase.java:227) > > > > > at com.hp.hpl.jena.tdb.store.GraphTDBBase > > > > > $MapperIteratorTriples.next(GraphTDBBase.java:186) > > > > > at org.topbraid.tdb.graphstore.AutoLockingTDBGraph > > > > > $2.next(AutoLockingTDBGraph.java:350) > > > > > at org.topbraid.tdb.graphstore.AutoLockingTDBGraph > > > > > $2.next(AutoLockingTDBGraph.java:1) > > > > > at > > > > > com.hp.hpl.jena.util.iterator.WrappedIterator.next(WrappedIterator.java: > > > > > 68) > > > > > at > > > > > com.hp.hpl.jena.util.iterator.FilterIterator.hasNext(FilterIterator.java: > > > > > 44) > > > > > at com.hp.hpl.jena.graph.compose.CompositionBase > > > > > $2.hasNext(CompositionBase.java:99) > > > > > at com.hp.hpl.jena.util.iterator.NiceIterator > > > > > $1.hasNext(NiceIterator.java:86) > > > > > at > > > > > com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java: > > > > > 64) > > > > > at > > > > > com.hp.hpl.jena.util.iterator.Map1Iterator.hasNext(Map1Iterator.java: > > > > > 38) > > > > > at > > > > > com.hp.hpl.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java: > > > > > 64) > > > > > at > > > > > org.topbraidcomposer.navigation.instances.InstancesTableContentProvider.addInstances(InstancesTableContentProvider.java: > > > > > 43) > > > > > at > > > > > org.topbraidcomposer.navigation.instances.InstancesTableContentProvider.getInstances(InstancesTableContentProvider.java: > > > > > 95) > > > > > at org.topbraidcomposer.navigation.instances.InstancesView > > > > > $12.run(InstancesView.java:627) > > > > > at org.eclipse.jface.operation.ModalContext > > > > > $ModalContextThread.run(ModalContext.java:121) > > > > > > -- > > > You received this message because you are subscribed to the Google > > > Group "TopBraid Suite Users", the topics of which include TopBraid > > > Composer, > > > TopBraid Live, TopBraid Ensemble, SPARQLMotion and SPIN. > > > To post to this group, send email to > > > [email protected] > > > To unsubscribe from this group, send email to > > > [email protected] > > > For more options, visit this group > > > athttp://groups.google.com/group/topbraid-users?hl=en > > > > -- > > You received this message because you are subscribed to the Google > > Group "TopBraid Suite Users", the topics of which include TopBraid Composer, > > TopBraid Live, TopBraid Ensemble, SPARQLMotion and SPIN. > > To post to this group, send email to > > [email protected] > > To unsubscribe from this group, send email to > > [email protected] > > For more options, visit this group at > > http://groups.google.com/group/topbraid-users?hl=en > -- > You received this message because you are subscribed to the Google > Group "TopBraid Suite Users", the topics of which include TopBraid Composer, > TopBraid Live, TopBraid Ensemble, SPARQLMotion and SPIN. > To post to this group, send email to > [email protected] > To unsubscribe from this group, send email to > [email protected] > For more options, visit this group at > http://groups.google.com/group/topbraid-users?hl=en -- You received this message because you are subscribed to the Google Group "TopBraid Suite Users", the topics of which include TopBraid Composer, TopBraid Live, TopBraid Ensemble, SPARQLMotion and SPIN. 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