Dear Owlim Devs,
I am having some problems with queries failing after restarts in safe
mode. The server shutdown cleanly and after restarting some queries fail.
I make sure the repository is shutdown cleanly using the following code.
@Override
public void shutDown()
throws SailException
{
super.shutDown();
log.info("Repository shutting down.");
while (! super.isShutDown())
{
try
{
Thread.sleep(TimeUnit.MINUTES.toMillis(1));
} catch (InterruptedException e)
{
if (super.isShutDown())
{
log.info("Repository shut down!");
return;
}
Thread.interrupted();
}
log.info("Repository still shutting down.");
}
}
I have a stack trace for the errors in case that could help debugging.
Regards,
Jerven
ERROR: ServletException
java.lang.RuntimeException: java.io.EOFException
at com.ontotext.trree.big.collections.a.g.if(Unknown Source)
at com.ontotext.trree.big.collections.a.m.a(Unknown Source)
at com.ontotext.trree.big.collections.a.b.a(Unknown Source)
at com.ontotext.trree.big.collections.a.p.do(Unknown Source)
at com.ontotext.trree.big.collections.l.a(Unknown Source)
at com.ontotext.trree.big.collections.l.a(Unknown Source)
at com.ontotext.trree.big.collections.l.a(Unknown Source)
at com.ontotext.trree.big.collections.p.if(Unknown Source)
at com.ontotext.trree.big.collections.p.do(Unknown Source)
at com.ontotext.trree.big.collections.j$a.a(Unknown Source)
at
com.ontotext.trree.big.AVLRepositoryConnection.getStatements(Unknown Source)
at
com.ontotext.trree.big.AVLRepositoryConnection.getStatements(Unknown Source)
at com.ontotext.trree.EqClassStatementIdIterator.byte(Unknown
Source)
at com.ontotext.trree.EqClassStatementIdIterator.next(Unknown
Source)
at com.ontotext.trree.EqClassStatementIdIterator.<init>(Unknown
Source)
at com.ontotext.trree.query.TriplePattern.getIterator(Unknown
Source)
at com.ontotext.trree.query.TriplePattern.getIterator(Unknown
Source)
at com.ontotext.trree.query.SubQuery.a(Unknown Source)
at com.ontotext.trree.query.SubQuery$3.next(Unknown Source)
at com.ontotext.trree.query.g$1.next(Unknown Source)
at com.ontotext.trree.query.q$2.a(Unknown Source)
at com.ontotext.trree.query.q$2.next(Unknown Source)
at com.ontotext.trree.sdk.a.d$2.hasNext(Unknown Source)
at
org.openrdf.query.algebra.evaluation.iterator.GroupIterator.buildEntries(GroupIterator.java:128)
at
org.openrdf.query.algebra.evaluation.iterator.GroupIterator.createIterator(GroupIterator.java:88)
at
org.openrdf.query.algebra.evaluation.iterator.GroupIterator.<init>(GroupIterator.java:78)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1208)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1068)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:177)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1178)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1059)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:177)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1071)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:177)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1132)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1044)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:177)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at
org.openrdf.query.algebra.evaluation.iterator.GroupIterator.buildEntries(GroupIterator.java:117)
at
org.openrdf.query.algebra.evaluation.iterator.GroupIterator.createIterator(GroupIterator.java:88)
at
org.openrdf.query.algebra.evaluation.iterator.GroupIterator.<init>(GroupIterator.java:78)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1208)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1068)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:177)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1178)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1059)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:177)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1132)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1044)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:177)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1159)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:1056)
at
org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:177)
at com.ontotext.trree.query.u.evaluate(Unknown Source)
at com.ontotext.trree.SailConnectionImpl.evaluate(Unknown
Source)
at
org.openrdf.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:48)
at
org.expasy.sesame.web.handlers.HTMLHandler._handle(HTMLHandler.java:69)
Caused by: java.io.EOFException
at java.io.RandomAccessFile.readInt(RandomAccessFile.java:776)
at com.ontotext.trree.big.collections.a.n.a(Unknown Source)
at com.ontotext.trree.big.collections.a.n.<init>(Unknown Source)
... 139 more
--
-------------------------------------------------------------------
Jerven Bolleman [email protected]
SIB Swiss Institute of Bioinformatics Tel: +41 (0)22 379 58 85
CMU, rue Michel Servet 1 Fax: +41 (0)22 379 58 58
1211 Geneve 4,
Switzerland www.isb-sib.ch - www.uniprot.org
Follow us at https://twitter.com/#!/uniprot
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