On 27/04/13 16:24, David Jordan wrote:
Tomorrow I will try to get into work, download the TDB source, set a breakpoint
on this FileException to try and diagnose this myself. This happens when I
first try to access a named Model in TDB that had been stored previously.
Unless there is a bug in TDB, I am guessing that this suggests that an earlier
transaction left the file in a corrupted state?
So what can cause TDB to get corrupted? Does every access need to be enclosed
in a transaction? If you are strictly reading the TDB database, do you need to
enclose all accesses in a read transaction, when you know there is no update
transactions? Is there a need to (always) call the sync() method? Does sync()
automatically get called when you commit or end a transaction? (I would hope
so.)
I have never examined TDB source before, it could take quiet a while to figure
out what is going wrong. Any suggestions for resolving this issue are greatly
appreciated.
On Apr 26, 2013, at 3:22 PM, David Jordan wrote:
I seem to randomly get the following file exception. Once I get this, I
continue to get it until I remove all the data for the model in question. I
reported this before, but I don’t believe I got any response. I am not sure
what is triggering this. The same code works fine for a while, and then this
happens.
http://mail-archives.apache.org/mod_mbox/jena-users/201304.mbox/%3C517AA3E5.7050609%40apache.org%3E
Once the node table is corrupted, it's permanently broken.
Using TDB (more generalised) transactions will protected better - Model
transactions are only a weak sync and a exit can cause problems.
When all the triple using that part of the node table, it'll appear to
work but add back a triple using a term that is broken and it'll reappear.
Andy
[junit] Caused by: com.hp.hpl.jena.tdb.base.file.FileException:
ObjectFileStorage.read[nodes.dat](30314841)[filesize=30315565][file.size()=30315565]:
Impossibly large object : 876033377 bytes > filesize-(loc+SizeOfInt)=720
[junit] at
com.hp.hpl.jena.tdb.base.objectfile.ObjectFileStorage.read(ObjectFileStorage.java:346)
[junit] at com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:78)
[junit] at
com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeFromTable(NodeTableNative.java:178)
[junit] at
com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
[junit] at
com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:74)
[junit] at
com.hp.hpl.jena.tdb.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:103)
[junit] at
com.hp.hpl.jena.tdb.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:74)
[junit] at
com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:55)
[junit] at
com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:67)
[junit] at com.hp.hpl.jena.tdb.lib.TupleLib.quad(TupleLib.java:159)
[junit] at com.hp.hpl.jena.tdb.lib.TupleLib.quad(TupleLib.java:153)
[junit] at com.hp.hpl.jena.tdb.lib.TupleLib.access$100(TupleLib.java:45)
[junit] at com.hp.hpl.jena.tdb.lib.TupleLib$4.convert(TupleLib.java:87)
[junit] at com.hp.hpl.jena.tdb.lib.TupleLib$4.convert(TupleLib.java:83)
[junit] at org.apache.jena.atlas.iterator.Iter$4.next(Iter.java:301)
[junit] at
com.hp.hpl.jena.tdb.store.GraphTDBBase$ProjectQuadsToTriples.next(GraphTDBBase.java:207)
[junit] at
com.hp.hpl.jena.tdb.store.GraphTDBBase$ProjectQuadsToTriples.next(GraphTDBBase.java:195)
[junit] at
com.hp.hpl.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
[junit] at
com.hp.hpl.jena.util.iterator.WrappedIterator.next(WrappedIterator.java:94)
[junit] at
com.hp.hpl.jena.mem.TrackingTripleIterator.next(TrackingTripleIterator.java:47)
[junit] at
com.hp.hpl.jena.mem.TrackingTripleIterator.next(TrackingTripleIterator.java:31)
[junit] at
com.hp.hpl.jena.reasoner.rulesys.impl.RETEEngine.fastInit(RETEEngine.java:151)
[junit] at
com.hp.hpl.jena.reasoner.rulesys.FBRuleInfGraph.prepare(FBRuleInfGraph.java:483)
[junit] at
com.hp.hpl.jena.ontology.impl.OntModelImpl.prepare(OntModelImpl.java:2694)
[junit] at
com.sas.ta.om.test.TestBase.setupConfiguration(TestBase.java:213)
[junit] at com.sas.ta.om.test.TestBase.<clinit>(TestBase.java:85)
[junit]
[junit]
[junit] TEST com.sas.ta.om.test.HasValueRestrictionOnPropertyTest FAILED
[junit] Running com.sas.ta.om.test.PreventAssigningInvalidPropertyValueTest
[junit] Testsuite:
com.sas.ta.om.test.PreventAssigningInvalidPropertyValueTest
[junit] Tests run: 1, Failures: 0, Errors: 1, Time elapsed: 0 sec
[junit] Tests run: 1, Failures: 0, Errors: 1, Time elapsed: 0 sec
[junit]
[junit] Null Test: Caused an ERROR
[junit] com.sas.ta.om.test.TestBase
[junit] java.lang.NoClassDefFoundError: com.sas.ta.om.test.TestBase
[junit] at java.lang.Class.forName0(Native Method)
David Jordan
Senior Software Developer
SAS Institute Inc.
Health & Life Sciences, Research & Development
Bldg R ▪ Office 4467
600 Research Drive ▪ Cary, NC 27513
Tel: 919 531 1233 ▪ [email protected]<mailto:[email protected]>
www.sas.com<http://www.sas.com/>
SAS® … THE POWER TO KNOW®
