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Posted to users@jena.apache.org by David Jordan <Da...@sas.com> on 2011/09/25 21:13:06 UTC
exception
I got the following exception using TDB-0.8.11-SNAPSHOT
[java] com.hp.hpl.jena.tdb.base.file.FileException: ObjectFile.read: Failed to read the object (795372659 bytes) : got 106 bytes
[java] at com.hp.hpl.jena.tdb.base.objectfile.ObjectFileDiskDirect.read(ObjectFileDiskDirect.java:182)
[java] at com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:70)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeByNodeId(NodeTableNative.java:158)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:85)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:58)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:44)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:55)
[java] at com.hp.hpl.jena.tdb.lib.TupleLib.tupleNodes(TupleLib.java:86)
[java] at com.hp.hpl.jena.tdb.lib.TupleLib$1.convert(TupleLib.java:40)
[java] at com.hp.hpl.jena.tdb.lib.TupleLib$1.convert(TupleLib.java:36)
[java] at org.openjena.atlas.iterator.Iter$4.next(Iter.java:268)
[java] at com.hp.hpl.jena.tdb.sys.ConcurrencyPolicyMRSW$IteratorCheckNotConcurrent.next(ConcurrencyPolicyMRSW.java:113)
[java] at com.hp.hpl.jena.tdb.store.DatasetPrefixesTDB.readPrefixMap(DatasetPrefixesTDB.java:157)
[java] at com.hp.hpl.jena.sparql.graph.GraphPrefixesProjection.getNsPrefixMap(GraphPrefixesProjection.java:51)
[java] at com.hp.hpl.jena.tdb.store.DatasetPrefixesTDB.getPrefixMapping(DatasetPrefixesTDB.java:207)
[java] at com.hp.hpl.jena.tdb.store.GraphNamedTDB.createPrefixMapping(GraphNamedTDB.java:65)
[java] at com.hp.hpl.jena.sparql.graph.GraphBase2.getPrefixMapping(GraphBase2.java:172)
[java] at com.hp.hpl.jena.rdf.model.impl.ModelCom.getPrefixMapping(ModelCom.java:769)
[java] at com.hp.hpl.jena.rdf.model.impl.ModelCom.withDefaultMappings(ModelCom.java:806)
[java] at com.hp.hpl.jena.rdf.model.impl.ModelCom.<init>(ModelCom.java:54)
[java] at com.hp.hpl.jena.rdf.model.impl.ModelCom.<init>(ModelCom.java:50)
[java] at com.hp.hpl.jena.rdf.model.ModelFactory.createModelForGraph(ModelFactory.java:146)
[java] at com.hp.hpl.jena.sparql.core.DatasetImpl.graph2model(DatasetImpl.java:113)
[java] at com.hp.hpl.jena.sparql.core.DatasetImpl.getNamedModel(DatasetImpl.java:75)
[java] at com.hp.hpl.jena.tdb.assembler.TDBGraphAssembler.open(TDBGraphAssembler.java:81)
[java] at com.hp.hpl.jena.tdb.assembler.TDBGraphAssembler.open(TDBGraphAssembler.java:29)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:118)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.open(AssemblerGroup.java:105)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$ExpandingAssemblerGroup.open(AssemblerGroup.java:69)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:37)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:34)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerGroup.openModel(AssemblerGroup.java:23)
[java] at com.sas.hls.hoa.ontology.Database.getICD9inferredModel(Database.java:28)
[java] at com.sas.hls.hoa.ontology.LoadPatientDiagnosis.main(LoadPatientDiagnosis.java:31)
[java] Exception in thread "main" com.hp.hpl.jena.assembler.exceptions.AssemblerException: caught: ObjectFile.read: Failed to read the object (795372659 bytes) : got 106 bytes
[java] doing:
[java] root: http://www.sas.com/hls/hoa#ICD9_inferred with type: http://jena.hpl.hp.com/2008/tdb#GraphTDB assembler class: class com.hp.hpl.jena.tdb.assembler.TDBGraphAssembler
[java]
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:126)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.open(AssemblerGroup.java:105)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$ExpandingAssemblerGroup.open(AssemblerGroup.java:69)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:37)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:34)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerGroup.openModel(AssemblerGroup.java:23)
[java] at com.sas.hls.hoa.ontology.Database.getICD9inferredModel(Database.java:28)
[java] at com.sas.hls.hoa.ontology.LoadPatientDiagnosis.main(LoadPatientDiagnosis.java:31)
[java] Caused by: com.hp.hpl.jena.tdb.base.file.FileException: ObjectFile.read: Failed to read the object (795372659 bytes) : got 106 bytes
[java] at com.hp.hpl.jena.tdb.base.objectfile.ObjectFileDiskDirect.read(ObjectFileDiskDirect.java:182)
[java] at com.hp.hpl.jena.tdb.lib.NodeLib.fetchDecode(NodeLib.java:70)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.readNodeByNodeId(NodeTableNative.java:158)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:85)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:58)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:44)
[java] at com.hp.hpl.jena.tdb.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:55)
[java] at com.hp.hpl.jena.tdb.lib.TupleLib.tupleNodes(TupleLib.java:86)
[java] at com.hp.hpl.jena.tdb.lib.TupleLib$1.convert(TupleLib.java:40)
[java] at com.hp.hpl.jena.tdb.lib.TupleLib$1.convert(TupleLib.java:36)
[java] at org.openjena.atlas.iterator.Iter$4.next(Iter.java:268)
[java] at com.hp.hpl.jena.tdb.sys.ConcurrencyPolicyMRSW$IteratorCheckNotConcurrent.next(ConcurrencyPolicyMRSW.java:113)
[java] at com.hp.hpl.jena.tdb.store.DatasetPrefixesTDB.readPrefixMap(DatasetPrefixesTDB.java:157)
[java] at com.hp.hpl.jena.sparql.graph.GraphPrefixesProjection.getNsPrefixMap(GraphPrefixesProjection.java:51)
[java] at com.hp.hpl.jena.tdb.store.DatasetPrefixesTDB.getPrefixMapping(DatasetPrefixesTDB.java:207)
[java] at com.hp.hpl.jena.tdb.store.GraphNamedTDB.createPrefixMapping(GraphNamedTDB.java:65)
[java] at com.hp.hpl.jena.sparql.graph.GraphBase2.getPrefixMapping(GraphBase2.java:172)
[java] at com.hp.hpl.jena.rdf.model.impl.ModelCom.getPrefixMapping(ModelCom.java:769)
[java] at com.hp.hpl.jena.rdf.model.impl.ModelCom.withDefaultMappings(ModelCom.java:806)
[java] at com.hp.hpl.jena.rdf.model.impl.ModelCom.<init>(ModelCom.java:54)
[java] at com.hp.hpl.jena.rdf.model.impl.ModelCom.<init>(ModelCom.java:50)
[java] at com.hp.hpl.jena.rdf.model.ModelFactory.createModelForGraph(ModelFactory.java:146)
[java] at com.hp.hpl.jena.sparql.core.DatasetImpl.graph2model(DatasetImpl.java:113)
[java] at com.hp.hpl.jena.sparql.core.DatasetImpl.getNamedModel(DatasetImpl.java:75)
[java] at com.hp.hpl.jena.tdb.assembler.TDBGraphAssembler.open(TDBGraphAssembler.java:81)
[java] at com.hp.hpl.jena.tdb.assembler.TDBGraphAssembler.open(TDBGraphAssembler.java:29)
[java] at com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:118)
[java] ... 7 more
[java] Java Result: 1
David Jordan
Software Developer
SAS Institute Inc.
Health & Life Sciences, Research & Development
Bldg R ▪ Office 4467
600 Research Drive ▪ Cary, NC 27513
Tel: 919 531 1233 ▪ david.jordan@sas.com<ma...@sas.com>
www.sas.com<http://www.sas.com>
SAS® … THE POWER TO KNOW®
RE: exception
Posted by David Jordan <Da...@sas.com>.
The prior close may have failed.
-----Original Message-----
From: Andy Seaborne [mailto:andy.seaborne.apache@gmail.com] On Behalf Of Andy Seaborne
Sent: Monday, September 26, 2011 7:23 AM
To: jena-users@incubator.apache.org
Subject: Re: exception
On 25/09/11 20:13, David Jordan wrote:
>
> I got the following exception using TDB-0.8.11-SNAPSHOT
>
> [java] com.hp.hpl.jena.tdb.base.file.FileException:
> ObjectFile.read: Failed to read the object (795372659 bytes) : got 106
> bytes
This (typically) occurs when the ObjectFile prefixes.dat is overwritten through either concurrent access with two active writers or two different JVMs accessing the same database.
It's possible TDB 0.8.11-SNAPSHOT has introduced a bug but the stacktrace does not give enough information. It says when it is detected, not when it happens which is usually different. You are opening a database - did the previous run close down properly?
Can you send me a test case (data and setup)?
Andy
Re: exception
Posted by Andy Seaborne <an...@apache.org>.
On 25/09/11 20:13, David Jordan wrote:
>
> I got the following exception using TDB-0.8.11-SNAPSHOT
>
> [java] com.hp.hpl.jena.tdb.base.file.FileException: ObjectFile.read: Failed to read the object (795372659 bytes) : got 106 bytes
This (typically) occurs when the ObjectFile prefixes.dat is overwritten
through either concurrent access with two active writers or two
different JVMs accessing the same database.
It's possible TDB 0.8.11-SNAPSHOT has introduced a bug but the
stacktrace does not give enough information. It says when it is
detected, not when it happens which is usually different. You are
opening a database - did the previous run close down properly?
Can you send me a test case (data and setup)?
Andy