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Posted to dev@jena.apache.org by "Andy Seaborne (JIRA)" <ji...@apache.org> on 2013/08/16 18:42:48 UTC
[jira] [Updated] (JENA-515) Incorrectly error message "Currently in
a transaction" when querying SPARQL
[ https://issues.apache.org/jira/browse/JENA-515?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Andy Seaborne updated JENA-515:
-------------------------------
Component/s: Fuseki
> Incorrectly error message "Currently in a transaction" when querying SPARQL
> ---------------------------------------------------------------------------
>
> Key: JENA-515
> URL: https://issues.apache.org/jira/browse/JENA-515
> Project: Apache Jena
> Issue Type: Bug
> Components: Fuseki, TDB
> Affects Versions: TDB 0.10.1
> Reporter: Knut-Olav Hoven
>
> This has happened after a OutOfMemoryError during import (batched import of 1000 resources per request).
> Fetching entire database with curl works OK:
> http://localhost:3030/ds/data?graph=sift-tprogram
> When querying with SPARQL I get an 500 error "Currently in a transaction".
> No other clients are active.
> Log output:
> {code}
> 15:27:01 INFO Fuseki :: [73] GET http://localhost:3030/ds/query?query=PREFIX+sift%3A+%3Chttp%3A%2F%2Fgluon.nrk.no%2F2013%2Fsift%23%3E%0D%0APREFIX+prog%3A+%3Chttp%3A%2F%2Fgluon.nrk.no%2F2013%2Fsift-program%23%3E%0D%0A%0D%0ASELECT+*%0D%0AFROM+%3Chttp%3A%2F%2Flocalhost%3A3030%2Fds%2Fdata%2Fsift-tprogram%3E%0D%0A%7B%0D%0A%3Fs+sift%3Akeys+%222005%2F02952%22+.%0D%0A%3Fs+%3Fp+%3Fo%0D%0A%7D%0D%0ALIMIT+1000&output=text&stylesheet=%2Fxml-to-html.xsl&force-accept=text%2Fplain
> 15:27:01 INFO Fuseki :: [73] Query = PREFIX sift: <http://gluon.nrk.no/2013/sift#> PREFIX prog: <http://gluon.nrk.no/2013/sift-program#> SELECT * FROM <http://localhost:3030/ds/data/sift-tprogram> { ?s sift:keys "2005/02952" . ?s ?p ?o } LIMIT 1000
> 15:27:02 WARN Fuseki :: [73] RC = 500 : Currently in a transaction (location:/home/n21759/var/jena-fuseki/db/)
> com.hp.hpl.jena.sparql.JenaTransactionException: Currently in a transaction (location:/home/n21759/var/jena-fuseki/db/)
> at com.hp.hpl.jena.tdb.transaction.DatasetGraphTransaction.checkNotActive(DatasetGraphTransaction.java:125)
> at com.hp.hpl.jena.sparql.core.DatasetGraphTrackActive.begin(DatasetGraphTrackActive.java:44)
> at org.apache.jena.fuseki.servlets.HttpAction.beginRead(HttpAction.java:118)
> at org.apache.jena.fuseki.servlets.SPARQL_Query.execute(SPARQL_Query.java:234)
> at org.apache.jena.fuseki.servlets.SPARQL_Query.executeWithParameter(SPARQL_Query.java:193)
> at org.apache.jena.fuseki.servlets.SPARQL_Query.perform(SPARQL_Query.java:78)
> at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:185)
> at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeAction(SPARQL_ServletBase.java:166)
> at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.execCommonWorker(SPARQL_ServletBase.java:154)
> at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:73)
> at org.apache.jena.fuseki.servlets.SPARQL_Query.doGet(SPARQL_Query.java:59)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:735)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
> at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
> at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1448)
> at org.eclipse.jetty.servlets.UserAgentFilter.doFilter(UserAgentFilter.java:82)
> at org.eclipse.jetty.servlets.GzipFilter.doFilter(GzipFilter.java:294)
> at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1419)
> at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:455)
> at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:229)
> at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1075)
> at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:384)
> at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
> at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1009)
> at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
> at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
> at org.eclipse.jetty.server.Server.handle(Server.java:370)
> at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:489)
> at org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:53)
> at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:949)
> at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1011)
> at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
> at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
> at org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:72)
> at org.eclipse.jetty.server.nio.BlockingChannelConnector$BlockingChannelEndPoint.run(BlockingChannelConnector.java:298)
> at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
> at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
> at java.lang.Thread.run(Thread.java:722)
> 15:27:02 INFO Fuseki :: [73] 500 Currently in a transaction (location:/home/n21759/var/jena-fuseki/db/) (601 ms)
> {code}
> Log message of the OutOfMemoryError:
> {code}
> java.lang.OutOfMemoryError: Java heap space
> Dumping heap to java_pid28296.hprof ...
> Heap dump file created [280365745 bytes in 2.986 secs]
> 15:10:27 WARN HttpAction :: Transaction still active in endWriter - no commit or abort seen (forced abort)
> 15:10:28 WARN HttpAction :: Exception in forced abort (trying to continue)
> 15:10:40 WARN Fuseki :: [66] RC = 500 : Java heap space
> java.lang.OutOfMemoryError: Java heap space
> at java.util.Arrays.copyOf(Arrays.java:2367)
> at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
> at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
> at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415)
> at java.lang.StringBuffer.append(StringBuffer.java:237)
> at java.io.StringWriter.write(StringWriter.java:112)
> at java.io.PrintWriter.write(PrintWriter.java:456)
> at java.io.PrintWriter.write(PrintWriter.java:473)
> at java.io.PrintWriter.print(PrintWriter.java:603)
> at java.io.PrintWriter.println(PrintWriter.java:756)
> at java.lang.Throwable$WrappedPrintWriter.println(Throwable.java:763)
> at java.lang.Throwable.printStackTrace(Throwable.java:657)
> at java.lang.Throwable.printStackTrace(Throwable.java:720)
> at org.apache.log4j.DefaultThrowableRenderer.render(DefaultThrowableRenderer.java:60)
> at org.apache.log4j.spi.ThrowableInformation.getThrowableStrRep(ThrowableInformation.java:87)
> at org.apache.log4j.spi.LoggingEvent.getThrowableStrRep(LoggingEvent.java:413)
> at org.apache.log4j.WriterAppender.subAppend(WriterAppender.java:313)
> at org.apache.log4j.WriterAppender.append(WriterAppender.java:162)
> at org.apache.log4j.AppenderSkeleton.doAppend(AppenderSkeleton.java:251)
> at org.apache.log4j.helpers.AppenderAttachableImpl.appendLoopOnAppenders(AppenderAttachableImpl.java:66)
> at org.apache.log4j.Category.callAppenders(Category.java:206)
> at org.apache.log4j.Category.forcedLog(Category.java:391)
> at org.apache.log4j.Category.log(Category.java:856)
> at org.slf4j.impl.Log4jLoggerAdapter.warn(Log4jLoggerAdapter.java:479)
> at org.apache.jena.atlas.logging.Log.warn(Log.java:160)
> at org.apache.jena.atlas.logging.Log.warn(Log.java:155)
> at org.apache.jena.fuseki.servlets.HttpAction.endWrite(HttpAction.java:156)
> at org.apache.jena.fuseki.servlets.SPARQL_REST_RW.doPost(SPARQL_REST_RW.java:97)
> at org.apache.jena.fuseki.servlets.SPARQL_REST.doPost$(SPARQL_REST.java:246)
> at org.apache.jena.fuseki.servlets.SPARQL_REST.dispatch(SPARQL_REST.java:203)
> at org.apache.jena.fuseki.servlets.SPARQL_REST.perform(SPARQL_REST.java:190)
> at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:185)
> 15:10:41 INFO Fuseki :: [66] 500 Java heap space (73.238 s)
> 15:10:41 INFO Fuseki :: [67] POST http://localhost:3030/ds/data?graph=sift-tprogram
> 15:11:06 WARN Fuseki :: [67] RC = 500 : Java heap space
> java.lang.OutOfMemoryError: Java heap space
> at java.util.Arrays.copyOfRange(Arrays.java:2694)
> at java.lang.String.<init>(String.java:203)
> at java.lang.StringBuilder.toString(StringBuilder.java:405)
> at org.apache.jena.riot.tokens.TokenizerText.readIRI(TokenizerText.java:477)
> at org.apache.jena.riot.tokens.TokenizerText.parseToken(TokenizerText.java:192)
> at org.apache.jena.riot.tokens.TokenizerText.hasNext(TokenizerText.java:89)
> at org.apache.jena.atlas.iterator.PeekIterator.fill(PeekIterator.java:50)
> at org.apache.jena.atlas.iterator.PeekIterator.next(PeekIterator.java:92)
> at org.apache.jena.riot.lang.LangEngine.nextToken(LangEngine.java:99)
> at org.apache.jena.riot.lang.LangEngine.expect(LangEngine.java:143)
> at org.apache.jena.riot.lang.LangEngine.expectOrEOF(LangEngine.java:128)
> at org.apache.jena.riot.lang.LangTurtleBase.expectEndOfTriplesTurtle(LangTurtleBase.java:258)
> at org.apache.jena.riot.lang.LangTurtle.expectEndOfTriples(LangTurtle.java:49)
> at org.apache.jena.riot.lang.LangTurtleBase.triples(LangTurtleBase.java:243)
> at org.apache.jena.riot.lang.LangTurtleBase.triplesSameSubject(LangTurtleBase.java:186)
> at org.apache.jena.riot.lang.LangTurtle.oneTopLevelElement(LangTurtle.java:44)
> at org.apache.jena.riot.lang.LangTurtleBase.runParser(LangTurtleBase.java:90)
> at org.apache.jena.riot.lang.LangBase.parse(LangBase.java:42)
> at org.apache.jena.fuseki.servlets.SPARQL_REST.parse(SPARQL_REST.java:417)
> at org.apache.jena.fuseki.servlets.SPARQL_REST.parseBody(SPARQL_REST.java:406)
> at org.apache.jena.fuseki.servlets.SPARQL_REST_RW.doPost(SPARQL_REST_RW.java:87)
> at org.apache.jena.fuseki.servlets.SPARQL_REST.doPost$(SPARQL_REST.java:246)
> at org.apache.jena.fuseki.servlets.SPARQL_REST.dispatch(SPARQL_REST.java:203)
> at org.apache.jena.fuseki.servlets.SPARQL_REST.perform(SPARQL_REST.java:190)
> at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeLifecycle(SPARQL_ServletBase.java:185)
> at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.executeAction(SPARQL_ServletBase.java:166)
> at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.execCommonWorker(SPARQL_ServletBase.java:154)
> at org.apache.jena.fuseki.servlets.SPARQL_ServletBase.doCommon(SPARQL_ServletBase.java:73)
> at org.apache.jena.fuseki.servlets.SPARQL_REST.service(SPARQL_REST.java:180)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
> at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
> at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1448)
> 15:11:06 INFO Fuseki :: [67] 500 Java heap space (25.723 s)
> {code}
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