[JENA-1619] TransactionException for large query results

• Type: Bug
• Status: Closed
• Priority: Major
• Resolution: Fixed
• Affects Version/s: Jena 3.9.0
• Fix Version/s: Jena 3.10.0
• Component/s: TDB2

Environment

MacOS 10.14
Java 1.8.0_161 (Oracle)

• Assignee: Andy Seaborne
• Reporter: Damien Obrist
• Created: 23/Oct/18 07:15
• Updated: 02/Jan/19 23:47
• Resolved: 25/Oct/18 16:56

Description

When querying a TDB2 dataset, I'm observing a suspicious TransactionException, even though the query results have been copied so they can be used outside of a transaction. The exception only seems to occur when there are many results.

Reproduction steps

• Sample dataset containing 1'000'000 triples
• Query all triples:

  SELECT * WHERE { ?s ?p ?o . }

• Copy query results for use outside of transaction:

  ResultSetFactory.copyResults(queryExecution.execSelect());

• Get any variable of the first result

All variables are null and the log shows the following exception:

org.apache.jena.dboe.transaction.txn.TransactionException: Not in a transaction
	at org.apache.jena.dboe.transaction.txn.TransactionalComponentLifecycle.checkTxn(TransactionalComponentLifecycle.java:417)
	at org.apache.jena.dboe.trans.data.TransBinaryDataFile.read(TransBinaryDataFile.java:182)
	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.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:222)
	at org.apache.thrift.TUnion$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.solver.BindingTDB.get1(BindingTDB.java:126)
	at org.apache.jena.sparql.engine.binding.BindingBase.get(BindingBase.java:104)
	at org.apache.jena.sparql.core.ResultBinding._get(ResultBinding.java:57)
	at org.apache.jena.sparql.core.QuerySolutionBase.get(QuerySolutionBase.java:33)
	at TransactionException.main(TransactionException.java:27)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:282)
	at java.lang.Thread.run(Thread.java:748)

I have created a minimal example available on GitHub and attached to this issue.

Findings

• The exception doesn't occur for smaller query results
• This seems to be a regression as it works as expected with Jena 3.8.0
• Using git bisect I have identified the commit where this starts to happen: 9a60253

Issue Links

• links to: GitHub Pull Request #482