Virtuoso 7 - problems when opening logs for dbpedia pipeline

tomas-knap commented 10 years ago

The following error occur when running dbpedia pipeline on top of Virtuoso 7 and then trying to browse logs. @janvojt Can you please reproduce on localhost?

It may be reproduced on dbpedia pipeline.

2014-02-19 10:29:46,456 [http-bio-8080-exec-498] ERROR cz.cuni.mff.xrg.odcs.frontend.AppEntry - Uncaught exception
java.lang.Error: java.lang.ClassCastException:java.lang.Short cannot be cast to openlink.util.Vector
    at virtuoso.jdbc4.VirtuosoConnection.read_request(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoFuture.nextResult(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoResultSet.process_result(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoResultSet.<init>(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoPreparedStatement.<init>(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoConnection.prepareStatement(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoConnection.prepareStatement(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at org.apache.commons.dbcp.DelegatingConnection.prepareStatement(DelegatingConnection.java:281) ~[commons-dbcp-1.4.jar:1.4]
    at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.prepareStatement(PoolingDataSource.java:313) ~[commons-dbcp-1.4.jar:1.4]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.prepareStatement(DatabaseAccessor.java:1556) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.prepareStatement(DatabaseAccessor.java:1505) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseCall.prepareStatement(DatabaseCall.java:778) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.basicExecuteCall(DatabaseAccessor.java:619) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.executeCall(DatabaseAccessor.java:558) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.sessions.AbstractSession.basicExecuteCall(AbstractSession.java:1991) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.sessions.server.ServerSession.executeCall(ServerSession.java:570) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.sessions.server.ClientSession.executeCall(ClientSession.java:250) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeCall(DatasourceCallQueryMechanism.java:242) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeCall(DatasourceCallQueryMechanism.java:228) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.selectOneRow(DatasourceCallQueryMechanism.java:714) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.ExpressionQueryMechanism.selectOneRowFromTable(ExpressionQueryMechanism.java:2801) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.ExpressionQueryMechanism.selectOneRow(ExpressionQueryMechanism.java:2754) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ReadObjectQuery.executeObjectLevelReadQuery(ReadObjectQuery.java:545) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeDatabaseQuery(ObjectLevelReadQuery.java:1168) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.DatabaseQuery.execute(DatabaseQuery.java:899) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ObjectLevelReadQuery.execute(ObjectLevelReadQuery.java:1127) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ReadObjectQuery.execute(ReadObjectQuery.java:431) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeInUnitOfWork(ObjectLevelReadQuery.java:1215) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:2896) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1793) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1775) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:129) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:116) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:89) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiateImpl(UnitOfWorkValueHolder.java:173) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiate(UnitOfWorkValueHolder.java:234) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:89) ~[commons-app-1.0.0.jar:na]
    at cz.cuni.mff.xrg.odcs.commons.app.execution.message.MessageRecord._persistence_get_dpuInstance(MessageRecord.java) ~[commons-app-1.0.0.jar:na]
    at cz.cuni.mff.xrg.odcs.commons.app.execution.message.MessageRecord.getDpuInstance(MessageRecord.java:117) ~[commons-app-1.0.0.jar:na]
    at cz.cuni.mff.xrg.odcs.frontend.container.accessor.MessageRecordAccessor.getValue(MessageRecordAccessor.java:80) ~[MessageRecordAccessor.class:na]
    at cz.cuni.mff.xrg.odcs.frontend.container.accessor.MessageRecordAccessor.getValue(MessageRecordAccessor.java:14) ~[MessageRecordAccessor.class:na]
    at cz.cuni.mff.xrg.odcs.frontend.container.GeneralProperty.getValueForObject(GeneralProperty.java:41) ~[GeneralProperty.class:na]
    at cz.cuni.mff.xrg.odcs.frontend.container.ValueProperty.getValue(ValueProperty.java:30) ~[ValueProperty.class:na]
    at com.vaadin.ui.CustomTable.formatPropertyValue(CustomTable.java:4062) ~[filteringtable-0.9.4.v7.jar:7.1.8]
    at com.vaadin.ui.CustomTable.getPropertyValue(CustomTable.java:4004) ~[filteringtable-0.9.4.v7.jar:7.1.8]
    at com.vaadin.ui.CustomTable.parseItemIdToCells(CustomTable.java:2341) ~[filteringtable-0.9.4.v7.jar:7.1.8]
    at com.vaadin.ui.CustomTable.getVisibleCellsNoCache(CustomTable.java:2174) ~[filteringtable-0.9.4.v7.jar:7.1.8]
    at com.vaadin.ui.CustomTable.refreshRenderedCells(CustomTable.java:1696) ~[filteringtable-0.9.4.v7.jar:7.1.8]
    at com.vaadin.ui.CustomTable.attach(CustomTable.java:4182) ~[filteringtable-0.9.4.v7.jar:7.1.8]
    at com.vaadin.server.AbstractClientConnector.attach(AbstractClientConnector.java:583) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.AbstractComponent.attach(AbstractComponent.java:572) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.AbstractClientConnector.attach(AbstractClientConnector.java:583) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.AbstractComponent.attach(AbstractComponent.java:572) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.AbstractClientConnector.attach(AbstractClientConnector.java:583) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.AbstractComponent.attach(AbstractComponent.java:572) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.AbstractClientConnector.attach(AbstractClientConnector.java:583) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.AbstractComponent.attach(AbstractComponent.java:572) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.AbstractClientConnector.attach(AbstractClientConnector.java:583) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.AbstractComponent.attach(AbstractComponent.java:572) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.AbstractClientConnector.attach(AbstractClientConnector.java:583) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.AbstractComponent.attach(AbstractComponent.java:572) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.AbstractComponent.setParent(AbstractComponent.java:479) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.AbstractComponentContainer.addComponent(AbstractComponentContainer.java:215) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.AbstractSplitPanel.setSecondComponent(AbstractSplitPanel.java:178) ~[vaadin-server-7.1.8.jar:7.1.8]
    at cz.cuni.mff.xrg.odcs.frontend.gui.views.executionlist.ExecutionListViewImpl.showExecutionDetail(ExecutionListViewImpl.java:115) ~[ExecutionListViewImpl.class:na]
    at cz.cuni.mff.xrg.odcs.frontend.gui.views.executionlist.ExecutionListPresenterImpl.showDebugEventHandler(ExecutionListPresenterImpl.java:179) ~[ExecutionListPresenterImpl.class:na]
    at cz.cuni.mff.xrg.odcs.frontend.gui.views.executionlist.ExecutionListViewImpl$14.itemClick(ExecutionListViewImpl.java:457) ~[ExecutionListViewImpl$14.class:na]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_40]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_40]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_40]
    at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_40]
    at com.vaadin.event.ListenerMethod.receiveEvent(ListenerMethod.java:508) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:167) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.AbstractClientConnector.fireEvent(AbstractClientConnector.java:969) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.ui.CustomTable.handleClickEvent(CustomTable.java:3065) ~[filteringtable-0.9.4.v7.jar:7.1.8]
    at com.vaadin.ui.CustomTable.changeVariables(CustomTable.java:2861) ~[filteringtable-0.9.4.v7.jar:7.1.8]
    at com.vaadin.server.communication.ServerRpcHandler.changeVariables(ServerRpcHandler.java:396) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.communication.ServerRpcHandler.handleBurst(ServerRpcHandler.java:221) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.communication.ServerRpcHandler.handleRpc(ServerRpcHandler.java:111) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.communication.UidlRequestHandler.synchronizedHandleRequest(UidlRequestHandler.java:91) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.SynchronizedRequestHandler.handleRequest(SynchronizedRequestHandler.java:37) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.VaadinService.handleRequest(VaadinService.java:1371) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:238) [vaadin-server-7.1.8.jar:7.1.8]
    at cz.cuni.mff.xrg.odcs.frontend.ODCSApplicationServlet.service(ODCSApplicationServlet.java:74) [ODCSApplicationServlet.class:na]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:728) [servlet-api.jar:na]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305) [catalina.jar:7.0.33]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [catalina.jar:7.0.33]
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222) [catalina.jar:7.0.33]
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123) [catalina.jar:7.0.33]
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472) [catalina.jar:7.0.33]
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171) [catalina.jar:7.0.33]
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99) [catalina.jar:7.0.33]
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:931) [catalina.jar:7.0.33]
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) [catalina.jar:7.0.33]
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407) [catalina.jar:7.0.33]
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1004) [tomcat-coyote.jar:7.0.33]
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589) [tomcat-coyote.jar:7.0.33]
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312) [tomcat-coyote.jar:7.0.33]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_40]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_40]
    at java.lang.Thread.run(Thread.java:724) [na:1.7.0_40]
2014-02-19 10:29:46,458 [http-bio-8080-exec-498] DEBUG org.eclipse.persistence.logging.sql - 2014-02-19 10:29:46.458--ServerSession(1269785031)--Connection(1267088754)--SELECT ID, config_valid, description, name, configuration, tool_tip, use_dpu_description, dpu_id FROM dpu_instance WHERE (ID = ?)
    bind => [100]
2014-02-19 10:29:46,460 [http-bio-8080-exec-498]

tomas-knap commented 10 years ago

Also it appears sometimes when opening pipeline detail:

    at java.lang.Thread.run(Thread.java:724) [na:1.7.0_40]
2014-02-19 10:39:24,326 [http-bio-8080-exec-495] DEBUG org.eclipse.persistence.logging.sql - 2014-02-19 10:39:24.326--ServerSession(1269785031)--Connection(176035214)--SELECT TOP 0,1 ID AS a1, opened AS a2, user_id AS a3, pipeline_id AS a4 FROM ppl_open_event WHERE ((user_id = ?) AND (pipeline_id = ?))
    bind => [1, 106]
2014-02-19 10:39:24,330 [http-bio-8080-exec-495] ERROR cz.cuni.mff.xrg.odcs.frontend.AppEntry - Uncaught exception
java.lang.Error: java.lang.ClassCastException:java.lang.Short cannot be cast to openlink.util.Vector
    at virtuoso.jdbc4.VirtuosoConnection.read_request(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoFuture.nextResult(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoResultSet.process_result(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoResultSet.<init>(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoPreparedStatement.<init>(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoConnection.prepareStatement(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at virtuoso.jdbc4.VirtuosoConnection.prepareStatement(Unknown Source) ~[virtjdbc-4.1.jar:na]
    at org.apache.commons.dbcp.DelegatingConnection.prepareStatement(DelegatingConnection.java:281) ~[commons-dbcp-1.4.jar:1.4]
    at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.prepareStatement(PoolingDataSource.java:313) ~[commons-dbcp-1.4.jar:1.4]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.prepareStatement(DatabaseAccessor.java:1556) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.prepareStatement(DatabaseAccessor.java:1505) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseCall.prepareStatement(DatabaseCall.java:778) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.basicExecuteCall(DatabaseAccessor.java:619) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.executeCall(DatabaseAccessor.java:558) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.sessions.AbstractSession.basicExecuteCall(AbstractSession.java:1991) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.sessions.server.ServerSession.executeCall(ServerSession.java:570) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.sessions.server.ClientSession.executeCall(ClientSession.java:250) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeCall(DatasourceCallQueryMechanism.java:242) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeCall(DatasourceCallQueryMechanism.java:228) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeSelectCall(DatasourceCallQueryMechanism.java:299) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.selectAllRows(DatasourceCallQueryMechanism.java:694) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.ExpressionQueryMechanism.selectAllRowsFromTable(ExpressionQueryMechanism.java:2738) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.queries.ExpressionQueryMechanism.selectAllRows(ExpressionQueryMechanism.java:2691) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ReadAllQuery.executeObjectLevelReadQuery(ReadAllQuery.java:495) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeDatabaseQuery(ObjectLevelReadQuery.java:1168) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.DatabaseQuery.execute(DatabaseQuery.java:899) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ObjectLevelReadQuery.execute(ObjectLevelReadQuery.java:1127) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ReadAllQuery.execute(ReadAllQuery.java:403) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeInUnitOfWork(ObjectLevelReadQuery.java:1215) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:2896) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1793) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1775) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1740) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.jpa.QueryImpl.executeReadQuery(QueryImpl.java:258) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.jpa.QueryImpl.getSingleResult(QueryImpl.java:517) ~[commons-app-1.0.0.jar:na]
    at org.eclipse.persistence.internal.jpa.EJBQueryImpl.getSingleResult(EJBQueryImpl.java:400) ~[commons-app-1.0.0.jar:na]
    at cz.cuni.mff.xrg.odcs.commons.app.dao.db.DbAccessReadBase.execute(DbAccessReadBase.java:119) ~[commons-app-1.0.0.jar:na]
    at cz.cuni.mff.xrg.odcs.commons.app.pipeline.DbOpenEventImpl.getOpenEvent(DbOpenEventImpl.java:29) ~[commons-app-1.0.0.jar:na]
    at cz.cuni.mff.xrg.odcs.commons.app.facade.PipelineFacadeImpl.createOpenEvent(PipelineFacadeImpl.java:246) ~[commons-app-1.0.0.jar:na]
    at sun.reflect.GeneratedMethodAccessor1230.invoke(Unknown Source) ~[na:na]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_40]
    at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_40]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:309) ~[spring-aop-3.0.7.RELEASE.jar:3.0.7.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:196) ~[spring-aop-3.0.7.RELEASE.jar:3.0.7.RELEASE]
    at com.sun.proxy.$Proxy493.createOpenEvent(Unknown Source) ~[na:na]
    at cz.cuni.mff.xrg.odcs.frontend.gui.views.PipelineEdit$1.refresh(PipelineEdit.java:180) ~[PipelineEdit$1.class:na]
    at com.github.wolfie.refresher.Refresher.fireRefreshEvents(Refresher.java:72) ~[refresher-1.2.1.7.jar:1.2.1.7]
    at com.github.wolfie.refresher.Refresher.access$1(Refresher.java:70) ~[refresher-1.2.1.7.jar:1.2.1.7]
    at com.github.wolfie.refresher.Refresher$1.refresh(Refresher.java:35) ~[refresher-1.2.1.7.jar:1.2.1.7]
    at sun.reflect.GeneratedMethodAccessor1214.invoke(Unknown Source) ~[na:na]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_40]
    at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_40]
    at com.vaadin.server.ServerRpcManager.applyInvocation(ServerRpcManager.java:168) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.ServerRpcManager.applyInvocation(ServerRpcManager.java:118) ~[vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.communication.ServerRpcHandler.handleBurst(ServerRpcHandler.java:207) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.communication.ServerRpcHandler.handleRpc(ServerRpcHandler.java:111) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.communication.UidlRequestHandler.synchronizedHandleRequest(UidlRequestHandler.java:91) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.SynchronizedRequestHandler.handleRequest(SynchronizedRequestHandler.java:37) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.VaadinService.handleRequest(VaadinService.java:1371) [vaadin-server-7.1.8.jar:7.1.8]
    at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:238) [vaadin-server-7.1.8.jar:7.1.8]
    at cz.cuni.mff.xrg.odcs.frontend.ODCSApplicationServlet.service(ODCSApplicationServlet.java:74) [ODCSApplicationServlet.class:na]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:728) [servlet-api.jar:na]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305) [catalina.jar:7.0.33]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [catalina.jar:7.0.33]
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222) [catalina.jar:7.0.33]
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123) [catalina.jar:7.0.33]
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472) [catalina.jar:7.0.33]
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171) [catalina.jar:7.0.33]
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99) [catalina.jar:7.0.33]
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:931) [catalina.jar:7.0.33]
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) [catalina.jar:7.0.33]
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407) [catalina.jar:7.0.33]
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1004) [tomcat-coyote.jar:7.0.33]
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589) [tomcat-coyote.jar:7.0.33]
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310) [tomcat-coyote.jar:7.0.33]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_40]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_40]
    at java.lang.Thread.run(Thread.java:724) [na:1.7.0_40]

tomas-knap commented 10 years ago

Otherwise Virtuoso 7 seems to be working fine

tomas-knap commented 10 years ago

This issue happens really often and has to be solved

janvojt commented 10 years ago

I cannot reproduce this. I tried running several parallel DBpedia runs in both normal and debug mode while browsing logs without any problem.

tomas-knap commented 10 years ago

which version of Virtuoso did you use?

Please test to connect to: v7.xrg.cz 1121 8901 dba/dba

This is the db where I experienced the problem

janvojt commented 10 years ago

This is my Virtuoso version:

11:56:25 OpenLink Virtuoso Universal Server
11:56:25 Version 07.00.3207-pthreads for Linux as of Dec 18 2013
11:56:25 uses parts of OpenSSL, PCRE, Html Tidy
11:56:26 Database version 3126

tomas-knap commented 10 years ago

Tak zkus prosim verzi 7.1., nedavno publikovana (tyden, dva zpatky)

Pripadne zkus prosim to virtuoso, co jsem psal

On Mon, Feb 24, 2014 at 12:11 PM, Jan Vojt notifications@github.com wrote:

This is my Virtuoso version:

11:56:25 OpenLink Virtuoso Universal Server 11:56:25 Version 07.00.3207-pthreads for Linux as of Dec 18 2013 11:56:25 uses parts of OpenSSL, PCRE, Html Tidy 11:56:26 Database version 3126

Reply to this email directly or view it on GitHubhttps://github.com/mff-uk/ODCS/issues/1235#issuecomment-35876505 .

janvojt commented 10 years ago

When connecting to v7.xrg.cz I also get NPE just before getting ClassCastException. This seems like a bug in JDBC. If I rememeber correctly, we already had this issue when trying Virtuoso 7.0 and it was resolved by upgrading JDBC to the latest version. @tomas-knap can you add the latest JDBC to nexus under next version number so we can try it?

Please do not just overwritethe old JDBC. I am emphasizing the next version so we have a stable version of JDBC on nexus when defending the project in 2 weeks.

org.springframework.orm.jpa.JpaSystemException: java.lang.NullPointerException; nested exception is javax.persistence.PersistenceException: java.lang.NullPointerException
        at org.springframework.orm.jpa.EntityManagerFactoryUtils.convertJpaAccessExceptionIfPossible(EntityManagerFactoryUtils.java:326) ~[spring-orm-3.1.2.RELEASE.jar:3.1.2.RELEASE]
        at org.springframework.orm.jpa.aspectj.JpaExceptionTranslatorAspect.ajc$afterThrowing$org_springframework_orm_jpa_aspectj_JpaExceptionTranslatorAspect$1$18a1ac9(JpaExceptionTranslatorAspect.aj:15) ~[spri
ng-aspects-3.1.2.RELEASE.jar:3.1.2.RELEASE]
        at cz.cuni.mff.xrg.odcs.commons.app.dao.db.DbAccessReadBase.execute(DbAccessReadBase.java:119) ~[commons-app-1.0.0.jar:na]
        at cz.cuni.mff.xrg.odcs.commons.app.dao.db.DbAccessReadBase.execute(DbAccessReadBase.java:54) ~[commons-app-1.0.0.jar:na]
        at cz.cuni.mff.xrg.odcs.commons.app.dao.db.DbAccessReadBase.execute(DbAccessReadBase.java:1) ~[commons-app-1.0.0.jar:na]
        at cz.cuni.mff.xrg.odcs.frontend.doa.container.db.DbCachedSource.loadByIndex(DbCachedSource.java:169) [DbCachedSource.class:na]
        at cz.cuni.mff.xrg.odcs.frontend.doa.container.db.DbCachedSource.loadByIndex(DbCachedSource.java:196) [DbCachedSource.class:na]
        at cz.cuni.mff.xrg.odcs.frontend.doa.container.db.DbCachedSource.getItemIds(DbCachedSource.java:370) [DbCachedSource.class:na]
        at cz.cuni.mff.xrg.odcs.frontend.container.ReadOnlyContainer.getItemIds(ReadOnlyContainer.java:259) [ReadOnlyContainer.class:na]
        at org.tepi.filtertable.paged.PagedFilterTableContainer.getItemIds(PagedFilterTableContainer.java:89) [filteringtable-0.9.4.v7.jar:0.9.4.v7]
        at com.vaadin.ui.CustomTable.getItemIds(CustomTable.java:2221) [filteringtable-0.9.4.v7.jar:7.1.8]
        at com.vaadin.ui.CustomTable.getVisibleCellsNoCache(CustomTable.java:2170) [filteringtable-0.9.4.v7.jar:7.1.8]
        at com.vaadin.ui.CustomTable.refreshRenderedCells(CustomTable.java:1696) [filteringtable-0.9.4.v7.jar:7.1.8]
        at com.vaadin.ui.CustomTable.enableContentRefreshing(CustomTable.java:3177) [filteringtable-0.9.4.v7.jar:7.1.8]
        at com.vaadin.ui.CustomTable.setContainerDataSource(CustomTable.java:2746) [filteringtable-0.9.4.v7.jar:7.1.8]
        at com.vaadin.ui.CustomTable.setContainerDataSource(CustomTable.java:2687) [filteringtable-0.9.4.v7.jar:7.1.8]
        at org.tepi.filtertable.FilterTable.setContainerDataSource(FilterTable.java:120) [filteringtable-0.9.4.v7.jar:0.9.4.v7]
        at org.tepi.filtertable.paged.PagedFilterTable.setContainerDataSource(PagedFilterTable.java:249) [filteringtable-0.9.4.v7.jar:0.9.4.v7]
        at cz.cuni.mff.xrg.odcs.frontend.gui.tables.IntlibPagedTable.setContainerDataSource(IntlibPagedTable.java:222) [IntlibPagedTable.class:na]
        at cz.cuni.mff.xrg.odcs.frontend.gui.tables.RecordsTable.setExecution(RecordsTable.java:119) [RecordsTable.class:na]
        at cz.cuni.mff.xrg.odcs.frontend.gui.components.DebuggingView.setExecution(DebuggingView.java:356) [DebuggingView.class:na]
        at cz.cuni.mff.xrg.odcs.frontend.gui.components.DebuggingView.setExecution(DebuggingView.java:330) [DebuggingView.class:na]
        at cz.cuni.mff.xrg.odcs.frontend.gui.views.executionlist.ExecutionListViewImpl.showExecutionDetail(ExecutionListViewImpl.java:115) [ExecutionListViewImpl.class:na]
        at cz.cuni.mff.xrg.odcs.frontend.gui.views.executionlist.ExecutionListPresenterImpl.showDebugEventHandler(ExecutionListPresenterImpl.java:180) [ExecutionListPresenterImpl.class:na]
        at cz.cuni.mff.xrg.odcs.frontend.gui.views.executionlist.ExecutionListViewImpl$14.itemClick(ExecutionListViewImpl.java:464) [ExecutionListViewImpl$14.class:na]
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_45]
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_45]
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_45]
        at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_45]
        at com.vaadin.event.ListenerMethod.receiveEvent(ListenerMethod.java:508) [vaadin-server-7.1.8.jar:7.1.8]
        at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:167) [vaadin-server-7.1.8.jar:7.1.8]
        at com.vaadin.server.AbstractClientConnector.fireEvent(AbstractClientConnector.java:969) [vaadin-server-7.1.8.jar:7.1.8]
        at com.vaadin.ui.CustomTable.handleClickEvent(CustomTable.java:3065) [filteringtable-0.9.4.v7.jar:7.1.8]
        at com.vaadin.ui.CustomTable.changeVariables(CustomTable.java:2861) [filteringtable-0.9.4.v7.jar:7.1.8]
        at com.vaadin.server.communication.ServerRpcHandler.changeVariables(ServerRpcHandler.java:396) [vaadin-server-7.1.8.jar:7.1.8]
        at com.vaadin.server.communication.ServerRpcHandler.handleBurst(ServerRpcHandler.java:221) [vaadin-server-7.1.8.jar:7.1.8]
        at com.vaadin.server.communication.ServerRpcHandler.handleRpc(ServerRpcHandler.java:111) [vaadin-server-7.1.8.jar:7.1.8]
        at com.vaadin.server.communication.UidlRequestHandler.synchronizedHandleRequest(UidlRequestHandler.java:91) [vaadin-server-7.1.8.jar:7.1.8]
        at com.vaadin.server.SynchronizedRequestHandler.handleRequest(SynchronizedRequestHandler.java:37) [vaadin-server-7.1.8.jar:7.1.8]
        at com.vaadin.server.VaadinService.handleRequest(VaadinService.java:1371) [vaadin-server-7.1.8.jar:7.1.8]
        at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:238) [vaadin-server-7.1.8.jar:7.1.8]
        at cz.cuni.mff.xrg.odcs.frontend.ODCSApplicationServlet.service(ODCSApplicationServlet.java:74) [ODCSApplicationServlet.class:na]
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:728) [servlet-api.jar:na]
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305) [catalina.jar:7.0.37]
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [catalina.jar:7.0.37]
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222) [catalina.jar:7.0.37]
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123) [catalina.jar:7.0.37]
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472) [catalina.jar:7.0.37]
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171) [catalina.jar:7.0.37]
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99) [catalina.jar:7.0.37]
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:936) [catalina.jar:7.0.37]
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) [catalina.jar:7.0.37]
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407) [catalina.jar:7.0.37]
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1004) [tomcat-coyote.jar:7.0.37]
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589) [tomcat-coyote.jar:7.0.37]
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312) [tomcat-coyote.jar:7.0.37]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_45]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_45]
        at java.lang.Thread.run(Thread.java:744) [na:1.7.0_45]
Caused by: javax.persistence.PersistenceException: java.lang.NullPointerException
        at org.eclipse.persistence.internal.jpa.QueryImpl.getSingleResult(QueryImpl.java:547) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.jpa.EJBQueryImpl.getSingleResult(EJBQueryImpl.java:400) ~[commons-app-1.0.0.jar:na]
        at sun.reflect.GeneratedMethodAccessor640.invoke(Unknown Source) ~[na:na]
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_45]
        at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_45]
        at org.springframework.orm.jpa.SharedEntityManagerCreator$DeferredQueryInvocationHandler.invoke(SharedEntityManagerCreator.java:310) ~[spring-orm-3.1.2.RELEASE.jar:3.1.2.RELEASE]
        at com.sun.proxy.$Proxy662.getSingleResult(Unknown Source) ~[na:na]
        ... 57 common frames omitted
Caused by: java.lang.NullPointerException: null
        at virtuoso.jdbc4.VirtuosoConnection.read_request(Unknown Source) ~[virtjdbc-4.1.jar:na]
        at virtuoso.jdbc4.VirtuosoFuture.nextResult(Unknown Source) ~[virtjdbc-4.1.jar:na]
        at virtuoso.jdbc4.VirtuosoResultSet.process_result(Unknown Source) ~[virtjdbc-4.1.jar:na]
        at virtuoso.jdbc4.VirtuosoResultSet.<init>(Unknown Source) ~[virtjdbc-4.1.jar:na]
        at virtuoso.jdbc4.VirtuosoPreparedStatement.<init>(Unknown Source) ~[virtjdbc-4.1.jar:na]
        at virtuoso.jdbc4.VirtuosoConnection.prepareStatement(Unknown Source) ~[virtjdbc-4.1.jar:na]
        at virtuoso.jdbc4.VirtuosoConnection.prepareStatement(Unknown Source) ~[virtjdbc-4.1.jar:na]
        at org.apache.commons.dbcp.DelegatingConnection.prepareStatement(DelegatingConnection.java:281) ~[commons-dbcp-1.4.jar:1.4]
        at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.prepareStatement(PoolingDataSource.java:313) ~[commons-dbcp-1.4.jar:1.4]
        at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.prepareStatement(DatabaseAccessor.java:1556) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.prepareStatement(DatabaseAccessor.java:1505) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.databaseaccess.DatabaseCall.prepareStatement(DatabaseCall.java:778) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.basicExecuteCall(DatabaseAccessor.java:619) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.databaseaccess.DatabaseAccessor.executeCall(DatabaseAccessor.java:558) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.sessions.AbstractSession.basicExecuteCall(AbstractSession.java:1991) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.sessions.server.ServerSession.executeCall(ServerSession.java:570) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.sessions.server.ClientSession.executeCall(ClientSession.java:250) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeCall(DatasourceCallQueryMechanism.java:242) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeCall(DatasourceCallQueryMechanism.java:228) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.executeSelectCall(DatasourceCallQueryMechanism.java:299) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.queries.DatasourceCallQueryMechanism.selectAllRows(DatasourceCallQueryMechanism.java:694) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.queries.ExpressionQueryMechanism.selectAllRowsFromTable(ExpressionQueryMechanism.java:2738) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.queries.ExpressionQueryMechanism.selectAllRows(ExpressionQueryMechanism.java:2691) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.queries.ReadAllQuery.executeObjectLevelReadQuery(ReadAllQuery.java:495) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeDatabaseQuery(ObjectLevelReadQuery.java:1168) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.queries.DatabaseQuery.execute(DatabaseQuery.java:899) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.queries.ObjectLevelReadQuery.execute(ObjectLevelReadQuery.java:1127) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.queries.ReadAllQuery.execute(ReadAllQuery.java:403) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeInUnitOfWork(ObjectLevelReadQuery.java:1215) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:2896) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1793) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1775) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1740) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.jpa.QueryImpl.executeReadQuery(QueryImpl.java:258) ~[commons-app-1.0.0.jar:na]
        at org.eclipse.persistence.internal.jpa.QueryImpl.getSingleResult(QueryImpl.java:517) ~[commons-app-1.0.0.jar:na]
        ... 63 common frames omitted

tomas-knap commented 10 years ago

Currently, we use:

com.openlinksw virtjdbc 4.1

tomas-knap commented 10 years ago

Nove jsem tam dal

com.openlinksw virtjdbc 4.1.1

Upravil jsem to u commons-app a rdf modulu. Zkusim na odcs-test

mff-uk / odcs

Virtuoso 7 - problems when opening logs for dbpedia pipeline #1235