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https://issues.apache.org/jira/browse/JENA-1758?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16930338#comment-16930338
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Andy Seaborne commented on JENA-1758:
-------------------------------------
{quote}I see the fix version is Jena 3.13.0. Do you have a rough estimate on
when it is going to be released?
{quote}
"Soon" :) We hope to release this month but everyone is fitting in the open
source work around everything else.
There are development builds if you want to try it out now or build locally.
The fix is in master now.
> Exception when preparing InfModel after TDB loading operation
> -------------------------------------------------------------
>
> Key: JENA-1758
> URL: https://issues.apache.org/jira/browse/JENA-1758
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
> Affects Versions: Jena 3.12.0
> Reporter: Damien Obrist
> Assignee: Andy Seaborne
> Priority: Critical
> Fix For: Jena 3.13.0
>
> Time Spent: 20m
> Remaining Estimate: 0h
>
> h2. Exception
> I'm loading a few million triples into a TDB2 dataset. I'm using a custom
> loader (extending {{LoaderMain}}), since the triples being loaded are
> generated by a separate application and streamed in over HTTP.
> After the loading is done, I try to reset an {{InfModel}} to recompute the
> inference taking into account the new triples, but I encounter the following
> exception:
> {noformat}
> org.apache.jena.atlas.RuntimeIOException: Out of bounds: (limit
> 32834204)32834205
> at org.apache.jena.atlas.io.IO.exception(IO.java:254)
> at
> org.apache.jena.dboe.trans.data.TransBinaryDataFile.checkRead(TransBinaryDataFile.java:190)
> at
> org.apache.jena.dboe.trans.data.TransBinaryDataFile.read(TransBinaryDataFile.java:184)
> at
> org.apache.jena.tdb2.store.nodetable.TReadAppendFileTransport.read(TReadAppendFileTransport.java:71)
> at org.apache.thrift.transport.TTransport.readAll(TTransport.java:86)
> at
> org.apache.thrift.protocol.TCompactProtocol.readByte(TCompactProtocol.java:637)
> at
> org.apache.thrift.protocol.TCompactProtocol.readFieldBegin(TCompactProtocol.java:543)
> at
> org.apache.jena.riot.thrift.wire.RDF_IRI$RDF_IRIStandardScheme.read(RDF_IRI.java:318)
> at
> org.apache.jena.riot.thrift.wire.RDF_IRI$RDF_IRIStandardScheme.read(RDF_IRI.java:311)
> at org.apache.jena.riot.thrift.wire.RDF_IRI.read(RDF_IRI.java:258)
> at
> org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:319)
> at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224)
> at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213)
> at org.apache.thrift.TUnion.read(TUnion.java:138)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:80)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:52)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:197)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:108)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:52)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:66)
> at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:112)
> at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:108)
> at
> org.apache.jena.tdb2.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:53)
> at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:270)
> at
> org.apache.jena.atlas.iterator.IteratorWrapper.next(IteratorWrapper.java:36)
> at
> org.apache.jena.tdb2.store.IteratorTxnTracker.next(IteratorTxnTracker.java:43)
> at
> java.util.Spliterators$IteratorSpliterator.tryAdvance(Spliterators.java:1812)
> at
> java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294)
> at
> java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206)
> at
> java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:169)
> at
> java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300)
> at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681)
> at org.apache.jena.atlas.iterator.Iter$2.hasNext(Iter.java:265)
> at org.apache.jena.atlas.iterator.Iter.hasNext(Iter.java:903)
> at org.apache.jena.atlas.iterator.Iter$1.hasNext(Iter.java:192)
> at
> org.apache.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
> at
> org.apache.jena.reasoner.rulesys.impl.RETEEngine.fastInit(RETEEngine.java:155)
> at
> org.apache.jena.reasoner.rulesys.FBRuleInfGraph.prepare(FBRuleInfGraph.java:471)
> at
> org.apache.jena.rdf.model.impl.InfModelImpl.prepare(InfModelImpl.java:87)
> ...
> {noformat}
> h2. Code
> I tried to come up with a minimal example but wasn't able to reproduce the
> issue outside of my more involved application environment, where the issue
> occurs consistently. It seems to depend on a specific timing, the number of
> triples being loaded, the inference rules used etc.
> The code looks roughly like this:
> {code:java}
> // initialize
> Dataset dataset = TDB2Factory.connectDataset(path);
> Model unionModel = dataset.getNamedModel("urn:x-arq:UnionGraph");
> InfModel infModel = ModelFactory.createInfModel(reasoner, unionModel);
> Txn.executeRead(dataset, infModel::prepare);
> // load
> InputStream inputStream = // incoming HTTP stream
> DataLoader loader = new CustomLoader(LoaderPlans.loaderPlanParallel,
> dataset.asDatasetGraph);
> loader.startBulk();
> try {
> RDFDataMgr.parse(loader.stream(), inputStream, RDFLanguages.NQUADS);
> loader.finishBulk();
> } catch (RuntimeException e) {
> loader.finishException(e);
> throw e;
> }
> // reset model to recompute inference
> Txn.executeRead(dataset, () -> {
> model.reset();
> model.prepare();
> });
> {code}
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