[jira] [Commented] (JENA-1619) TransactionException for large query results
[
https://issues.apache.org/jira/browse/JENA-1619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16667430#comment-16667430
]
Damien Obrist commented on JENA-1619:
-
[~andy.seaborne] thanks for the fix! I can confirm that with the latest
3.10.0-SNAPSHOT the issue is resolved.
> TransactionException for large query results
>
>
> Key: JENA-1619
> URL: https://issues.apache.org/jira/browse/JENA-1619
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
>Affects Versions: Jena 3.9.0
> Environment: MacOS 10.14
> Java 1.8.0_161 (Oracle)
>Reporter: Damien Obrist
>Assignee: Andy Seaborne
>Priority: Major
> Fix For: Jena 3.10.0
>
> Attachments: jena-transaction-exception-master.zip
>
>
> 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.
> h3. Reproduction steps
> * Sample dataset containing 1'000'000 triples
> * Query all triples:
> {code:java}
> SELECT * WHERE { ?s ?p ?o . }{code}
> * Copy query results for use outside of transaction:
> {code:java}
> ResultSetFactory.copyResults(queryExecution.execSelect());{code}
> * Get any variable of the first result
> All variables are {{null}} and the log shows the following exception:
> {noformat}
> 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)
> {noformat}
> I have created a minimal example available on
> [GitHub|https://github.com/dobrist/jena-transaction-exception] and attached
> to this issue.
> h3. 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|https://github.com/apache/jena/commit/9a60253c00aec6763adbb0253588fe4dc0b484d4]
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[jira] [Commented] (JENA-1619) TransactionException for large query results
[
https://issues.apache.org/jira/browse/JENA-1619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16664014#comment-16664014
]
ASF GitHub Bot commented on JENA-1619:
--
Github user asfgit closed the pull request at:
https://github.com/apache/jena/pull/482
> TransactionException for large query results
>
>
> Key: JENA-1619
> URL: https://issues.apache.org/jira/browse/JENA-1619
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
>Affects Versions: Jena 3.9.0
> Environment: MacOS 10.14
> Java 1.8.0_161 (Oracle)
>Reporter: Damien Obrist
>Priority: Major
> Attachments: jena-transaction-exception-master.zip
>
>
> 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.
> h3. Reproduction steps
> * Sample dataset containing 1'000'000 triples
> * Query all triples:
> {code:java}
> SELECT * WHERE { ?s ?p ?o . }{code}
> * Copy query results for use outside of transaction:
> {code:java}
> ResultSetFactory.copyResults(queryExecution.execSelect());{code}
> * Get any variable of the first result
> All variables are {{null}} and the log shows the following exception:
> {noformat}
> 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)
> {noformat}
> I have created a minimal example available on
> [GitHub|https://github.com/dobrist/jena-transaction-exception] and attached
> to this issue.
> h3. 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|https://github.com/apache/jena/commit/9a60253c00aec6763adbb0253588fe4dc0b484d4]
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[jira] [Commented] (JENA-1619) TransactionException for large query results
[
https://issues.apache.org/jira/browse/JENA-1619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16664012#comment-16664012
]
ASF subversion and git services commented on JENA-1619:
---
Commit c3027d69ac87763113322876816fb6292ef6cd6a in jena's branch
refs/heads/master from [~an...@apache.org]
[ https://git-wip-us.apache.org/repos/asf?p=jena.git;h=c3027d6 ]
JENA-1619: Merge commit 'refs/pull/482/head' of https://github.com/apache/jena
This closes #482.
> TransactionException for large query results
>
>
> Key: JENA-1619
> URL: https://issues.apache.org/jira/browse/JENA-1619
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
>Affects Versions: Jena 3.9.0
> Environment: MacOS 10.14
> Java 1.8.0_161 (Oracle)
>Reporter: Damien Obrist
>Priority: Major
> Attachments: jena-transaction-exception-master.zip
>
>
> 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.
> h3. Reproduction steps
> * Sample dataset containing 1'000'000 triples
> * Query all triples:
> {code:java}
> SELECT * WHERE { ?s ?p ?o . }{code}
> * Copy query results for use outside of transaction:
> {code:java}
> ResultSetFactory.copyResults(queryExecution.execSelect());{code}
> * Get any variable of the first result
> All variables are {{null}} and the log shows the following exception:
> {noformat}
> 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)
> {noformat}
> I have created a minimal example available on
> [GitHub|https://github.com/dobrist/jena-transaction-exception] and attached
> to this issue.
> h3. 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|https://github.com/apache/jena/commit/9a60253c00aec6763adbb0253588fe4dc0b484d4]
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[jira] [Commented] (JENA-1619) TransactionException for large query results
[
https://issues.apache.org/jira/browse/JENA-1619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16664010#comment-16664010
]
ASF subversion and git services commented on JENA-1619:
---
Commit cd75e6c1597db5da1adf2eb3decd5bd59877b266 in jena's branch
refs/heads/master from [~an...@apache.org]
[ https://git-wip-us.apache.org/repos/asf?p=jena.git;h=cd75e6c ]
JENA-1619: Completely detach a binding by doing a copy.
> TransactionException for large query results
>
>
> Key: JENA-1619
> URL: https://issues.apache.org/jira/browse/JENA-1619
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
>Affects Versions: Jena 3.9.0
> Environment: MacOS 10.14
> Java 1.8.0_161 (Oracle)
>Reporter: Damien Obrist
>Priority: Major
> Attachments: jena-transaction-exception-master.zip
>
>
> 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.
> h3. Reproduction steps
> * Sample dataset containing 1'000'000 triples
> * Query all triples:
> {code:java}
> SELECT * WHERE { ?s ?p ?o . }{code}
> * Copy query results for use outside of transaction:
> {code:java}
> ResultSetFactory.copyResults(queryExecution.execSelect());{code}
> * Get any variable of the first result
> All variables are {{null}} and the log shows the following exception:
> {noformat}
> 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)
> {noformat}
> I have created a minimal example available on
> [GitHub|https://github.com/dobrist/jena-transaction-exception] and attached
> to this issue.
> h3. 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|https://github.com/apache/jena/commit/9a60253c00aec6763adbb0253588fe4dc0b484d4]
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[jira] [Commented] (JENA-1619) TransactionException for large query results
[
https://issues.apache.org/jira/browse/JENA-1619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16664011#comment-16664011
]
ASF subversion and git services commented on JENA-1619:
---
Commit c89ed1238bcee69918e7aeedaf52637c66ff315c in jena's branch
refs/heads/master from [~an...@apache.org]
[ https://git-wip-us.apache.org/repos/asf?p=jena.git;h=c89ed12 ]
JENA-1619: Don't materialize bindings.
No need to materialize.
Bindings aren't safe outside a transaction anyway.
> TransactionException for large query results
>
>
> Key: JENA-1619
> URL: https://issues.apache.org/jira/browse/JENA-1619
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
>Affects Versions: Jena 3.9.0
> Environment: MacOS 10.14
> Java 1.8.0_161 (Oracle)
>Reporter: Damien Obrist
>Priority: Major
> Attachments: jena-transaction-exception-master.zip
>
>
> 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.
> h3. Reproduction steps
> * Sample dataset containing 1'000'000 triples
> * Query all triples:
> {code:java}
> SELECT * WHERE { ?s ?p ?o . }{code}
> * Copy query results for use outside of transaction:
> {code:java}
> ResultSetFactory.copyResults(queryExecution.execSelect());{code}
> * Get any variable of the first result
> All variables are {{null}} and the log shows the following exception:
> {noformat}
> 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)
> {noformat}
> I have created a minimal example available on
> [GitHub|https://github.com/dobrist/jena-transaction-exception] and attached
> to this issue.
> h3. 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|https://github.com/apache/jena/commit/9a60253c00aec6763adbb0253588fe4dc0b484d4]
--
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[jira] [Commented] (JENA-1619) TransactionException for large query results
[
https://issues.apache.org/jira/browse/JENA-1619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16662355#comment-16662355
]
Andy Seaborne commented on JENA-1619:
-
The solution in the PR is to do a proper binding copy to properly detacts the
result from the transaction.
Some legacy code (which shouldn't have got copied into TDB2) can be removed.
This may affect some non-transactional (and not recommended) use of TDB1,
although the impact is on already unsafe code.
> TransactionException for large query results
>
>
> Key: JENA-1619
> URL: https://issues.apache.org/jira/browse/JENA-1619
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
>Affects Versions: Jena 3.9.0
> Environment: MacOS 10.14
> Java 1.8.0_161 (Oracle)
>Reporter: Damien Obrist
>Priority: Major
> Attachments: jena-transaction-exception-master.zip
>
>
> 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.
> h3. Reproduction steps
> * Sample dataset containing 1'000'000 triples
> * Query all triples:
> {code:java}
> SELECT * WHERE { ?s ?p ?o . }{code}
> * Copy query results for use outside of transaction:
> {code:java}
> ResultSetFactory.copyResults(queryExecution.execSelect());{code}
> * Get any variable of the first result
> All variables are {{null}} and the log shows the following exception:
> {noformat}
> 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)
> {noformat}
> I have created a minimal example available on
> [GitHub|https://github.com/dobrist/jena-transaction-exception] and attached
> to this issue.
> h3. 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|https://github.com/apache/jena/commit/9a60253c00aec6763adbb0253588fe4dc0b484d4]
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[jira] [Commented] (JENA-1619) TransactionException for large query results
[
https://issues.apache.org/jira/browse/JENA-1619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16662346#comment-16662346
]
ASF GitHub Bot commented on JENA-1619:
--
GitHub user afs opened a pull request:
https://github.com/apache/jena/pull/482
JENA-1619: Completely detach results by copying a binding.
cd75e6c fixes the presenting problem.
c89ed12 removes a related non-working feature in TDB1/TDB2.
4dc260e is reformatting.
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/afs/jena binding-copy
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/jena/pull/482.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #482
commit cd75e6c1597db5da1adf2eb3decd5bd59877b266
Author: Andy Seaborne
Date: 2018-10-24T13:31:36Z
JENA-1619: Completely detach a binding by doing a copy.
commit c89ed1238bcee69918e7aeedaf52637c66ff315c
Author: Andy Seaborne
Date: 2018-10-24T13:34:05Z
JENA-1619: Don't materialize bindings.
No need to materialize.
Bindings aren't safe outside a transaction anyway.
commit 4dc260eeb2f627f724f6a382f42819f3c9b51cd6
Author: Andy Seaborne
Date: 2018-10-24T13:34:26Z
Cleanup formatting.
> TransactionException for large query results
>
>
> Key: JENA-1619
> URL: https://issues.apache.org/jira/browse/JENA-1619
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
>Affects Versions: Jena 3.9.0
> Environment: MacOS 10.14
> Java 1.8.0_161 (Oracle)
>Reporter: Damien Obrist
>Priority: Major
> Attachments: jena-transaction-exception-master.zip
>
>
> 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.
> h3. Reproduction steps
> * Sample dataset containing 1'000'000 triples
> * Query all triples:
> {code:java}
> SELECT * WHERE { ?s ?p ?o . }{code}
> * Copy query results for use outside of transaction:
> {code:java}
> ResultSetFactory.copyResults(queryExecution.execSelect());{code}
> * Get any variable of the first result
> All variables are {{null}} and the log shows the following exception:
> {noformat}
> 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)
>
[jira] [Commented] (JENA-1619) TransactionException for large query results
[
https://issues.apache.org/jira/browse/JENA-1619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16661831#comment-16661831
]
Damien Obrist commented on JENA-1619:
-
You're welcome.
Indeed this is an interesting one :)
This makes sense and would explain the size factor. When I tried to debug why
the changes in
[9a60253|https://github.com/apache/jena/commit/9a60253c00aec6763adbb0253588fe4dc0b484d4]
would lead to this new behavior I noticed the node table cache and suspected
it might have something to do with it. But I wasn't able to pinpoint the issue.
> TransactionException for large query results
>
>
> Key: JENA-1619
> URL: https://issues.apache.org/jira/browse/JENA-1619
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
>Affects Versions: Jena 3.9.0
> Environment: MacOS 10.14
> Java 1.8.0_161 (Oracle)
>Reporter: Damien Obrist
>Priority: Major
> Attachments: jena-transaction-exception-master.zip
>
>
> 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.
> h3. Reproduction steps
> * Sample dataset containing 1'000'000 triples
> * Query all triples:
> {code:java}
> SELECT * WHERE { ?s ?p ?o . }{code}
> * Copy query results for use outside of transaction:
> {code:java}
> ResultSetFactory.copyResults(queryExecution.execSelect());{code}
> * Get any variable of the first result
> All variables are {{null}} and the log shows the following exception:
> {noformat}
> 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)
> {noformat}
> I have created a minimal example available on
> [GitHub|https://github.com/dobrist/jena-transaction-exception] and attached
> to this issue.
> h3. 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|https://github.com/apache/jena/commit/9a60253c00aec6763adbb0253588fe4dc0b484d4]
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[jira] [Commented] (JENA-1619) TransactionException for large query results
[
https://issues.apache.org/jira/browse/JENA-1619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16660989#comment-16660989
]
Andy Seaborne commented on JENA-1619:
-
Thank you very much for the report.
On first reading, all I can say is that it is bizarre :-)
The size element maybe whether the node is in the NodeTableCache - the error is
a node table cache miss. If that is the reason, the beginning of a copied
result is more vulnerable (it is earlier and will be more at risk of
cache-replacement).
> TransactionException for large query results
>
>
> Key: JENA-1619
> URL: https://issues.apache.org/jira/browse/JENA-1619
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
>Affects Versions: Jena 3.9.0
> Environment: MacOS 10.14
> Java 1.8.0_161 (Oracle)
>Reporter: Damien Obrist
>Priority: Major
> Attachments: jena-transaction-exception-master.zip
>
>
> 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.
> h3. Reproduction steps
> * Sample dataset containing 1'000'000 triples
> * Query all triples:
> {code:java}
> SELECT * WHERE { ?s ?p ?o . }{code}
> * Copy query results for use outside of transaction:
> {code:java}
> ResultSetFactory.copyResults(queryExecution.execSelect());{code}
> * Get any variable of the first result
> All variables are {{null}} and the log shows the following exception:
> {noformat}
> 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)
> {noformat}
> I have created a minimal example available on
> [GitHub|https://github.com/dobrist/jena-transaction-exception] and attached
> to this issue.
> h3. 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|https://github.com/apache/jena/commit/9a60253c00aec6763adbb0253588fe4dc0b484d4]
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