John,
I tried your use case on TBC-ME 3.6.0B with one default graph and two
named graphs in a memory-store type Sesame 2.6.2 repository. I deleted
and saved a class from the default graph. I didn't get any errors, and
it worked fine.
TBC only exports a graph to Sesame through the TBC Export wizard. There
is no other export used. For other operations, TBC doesn't use any
queries, it simply adds or deletes triples. Since TBC is Jena-based,
also it has wrappers around Sesame Java library classes.
Your error seems to be caused by an interaction between OWLIM and
Sesame. In order to isolate the error, I would suggest doing a "remove"
of the class triples directly at the OpenRDF workbench for your Sesame
DB. You can do a remove under "Modify" section there. This might help if
it is a TBC-related issue, Sesame-related issue or OWLIM-related issue.
Gokhan
On 2/16/2012 11:40 AM, John Perdoni wrote:
Hi yesterday I sucessuflly created three connections to a sesame
repostory, one to the root graph and two to named graphs. Whilst
testing connectivity to the root graph I deleted (via tbc (right click
delete) a subclass that was in the root graph. I immediately got the
following error and now when trying to reconnect or trying to
reacreate the connection to the root graph, I persitantly get this
error Both connections to the named graphs are fine and any queries
to the named graph are fine as well. queries via the openrdf-sesame
workbench are fine and I dont seem to have any problems with the
repository itself.
I have been in touch with owlim forum and they have deduced that it is
an export problem, how does the tbc connector work, does it send a
query to export the whole graph, if so what is the query used. Does
tbc cache data anywhere ? is it possible you could supply me with the
configuration parameters of the connector so that I can pass them on
to owlim
Thanks in advance
John
Error from TBC
com.hp.hpl.jena.shared.ClosedException: Sesame reports
org.openrdf.repository.RepositoryException: <html><head><title>Apache
Tomcat/7.0.20 - Error report</title><style><!--H1
{font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;}
H2
{font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;}
H3
{font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;}
BODY
{font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;}
B
{font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;}
P
{font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A
{color : black;}A.name {color : black;}HR {color :
#525D76;}--></style> </head><body><h1>HTTP Status 500 - </h1><HR
size="1" noshade="noshade"><p><b>type</b> Exception
report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>The
server encountered an internal error () that prevented it from
fulfilling this request.</u></p><p><b>exception</b>
<pre>org.springframework.web.util.NestedServletException: Request
processing failed; nested exception is
java.lang.ArrayIndexOutOfBoundsException: -1
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:583)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:501)
javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
</pre></p><p><b>root cause</b>
<pre>java.lang.ArrayIndexOutOfBoundsException: -1
com.ontotext.trree.owlim_ext.c$2.next(Unknown Source)
com.ontotext.trree.owlim_ext.Repository$b.next(Unknown Source)
com.ontotext.trree.owlim_ext.Repository$a.next(Unknown Source)
com.ontotext.trree.owlim_ext.h$d.if(Unknown Source)
com.ontotext.trree.owlim_ext.h$d.a(Unknown Source)
com.ontotext.trree.owlim_ext.h$d.next(Unknown Source)
info.aduna.iteration.ExceptionConvertingIteration.next(ExceptionConvertingIteration.java:87)
org.openrdf.repository.RepositoryResult.next(RepositoryResult.java:61)
org.openrdf.repository.sail.SailRepositoryConnection.exportStatements(SailRepositoryConnection.java:223)
org.openrdf.http.server.repository.statements.ExportStatementsView.render(ExportStatementsView.java:99)
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1183)
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:902)
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:807)
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:571)
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:501)
javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
</pre></p><p><b>note</b> <u>The full stack trace of the root cause is
available in the Apache Tomcat/7.0.20 logs.</u></p><HR size="1"
noshade="noshade"><h3>Apache Tomcat/7.0.20</h3></body></html>
at
org.topbraid.sesame2.graph.RepositoryGraph.graphBaseFind(RepositoryGraph.java:99)
at com.hp.hpl.jena.graph.impl.GraphBase.find(GraphBase.java:240)
at
org.topbraid.core.graph.DelegatingGraph.delegateFind(DelegatingGraph.java:243)
at
org.topbraid.core.graph.CachingGraph.addToCache(CachingGraph.java:146)
at
org.topbraid.core.graph.AbstractCachingGraph.find(AbstractCachingGraph.java:178)
at
org.topbraid.core.graph.AbstractCachingGraph.find(AbstractCachingGraph.java:168)
at
org.topbraid.core.graph.DelegatingGraph.find(DelegatingGraph.java:113)
at
org.topbraid.core.graph.BufferingGraph.find(BufferingGraph.java:358)
at
org.topbraid.core.graph.BufferingGraph.find(BufferingGraph.java:379)
at
com.hp.hpl.jena.graph.compose.MultiUnion.multiGraphFind(MultiUnion.java:187)
at
com.hp.hpl.jena.graph.compose.MultiUnion.graphBaseFind(MultiUnion.java:166)
at com.hp.hpl.jena.graph.impl.GraphBase.find(GraphBase.java:240)
at
com.hp.hpl.jena.graph.impl.GraphBase.graphBaseFind(GraphBase.java:260)
at com.hp.hpl.jena.graph.impl.GraphBase.find(GraphBase.java:257)
at
com.hp.hpl.jena.rdf.model.impl.ModelCom.listStatements(ModelCom.java:378)
at
com.hp.hpl.jena.rdf.model.impl.ModelCom.listStatements(ModelCom.java:383)
at
com.hp.hpl.jena.rdf.model.impl.ResourceImpl.listProperties(ResourceImpl.java:160)
at
org.topbraid.forms.model.FormsUtil.getRelevantPropertiesOfInstance(FormsUtil.java:796)
at
org.topbraidcomposer.editors.forms.page.ResourceFormPage.getRelevantPredicates(ResourceFormPage.java:756)
at
org.topbraidcomposer.editors.forms.page.ResourceFormPage.addAll(ResourceFormPage.java:199)
at
org.topbraidcomposer.editors.forms.page.ResourceFormPage.createFormContent(ResourceFormPage.java:584)
at org.eclipse.ui.forms.editor.FormPage$1.run(FormPage.java:152)
at
org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at
org.eclipse.ui.forms.editor.FormPage.createPartControl(FormPage.java:150)
at
org.eclipse.ui.forms.editor.FormEditor.pageChange(FormEditor.java:471)
at
org.eclipse.ui.part.MultiPageEditorPart.setActivePage(MultiPageEditorPart.java:1067)
at
org.eclipse.ui.forms.editor.FormEditor.setActivePage(FormEditor.java:603)
at
org.eclipse.ui.part.MultiPageEditorPart.createPartControl(MultiPageEditorPart.java:352)
at
org.eclipse.ui.internal.EditorReference.createPartHelper(EditorReference.java:670)
at
org.eclipse.ui.internal.EditorReference.createPart(EditorReference.java:465)
at
org.eclipse.ui.internal.WorkbenchPartReference.getPart(WorkbenchPartReference.java:595)
at
org.eclipse.ui.internal.EditorReference.getEditor(EditorReference.java:289)
at
org.eclipse.ui.internal.WorkbenchPage.busyOpenEditorBatched(WorkbenchPage.java:2945)
at
org.eclipse.ui.internal.WorkbenchPage.busyOpenEditor(WorkbenchPage.java:2850)
at
org.eclipse.ui.internal.WorkbenchPage.access$11(WorkbenchPage.java:2842)
at
org.eclipse.ui.internal.WorkbenchPage$10.run(WorkbenchPage.java:2793)
at
org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at
org.eclipse.ui.internal.WorkbenchPage.openEditor(WorkbenchPage.java:2789)
at
org.eclipse.ui.internal.WorkbenchPage.openEditor(WorkbenchPage.java:2773)
at
org.topbraidcomposer.editors.ResourceEditorLauncher.openResourceEditor(ResourceEditorLauncher.java:652)
at
org.topbraidcomposer.editors.ResourceEditorLauncher.access$5(ResourceEditorLauncher.java:620)
at
org.topbraidcomposer.editors.ResourceEditorLauncher$6.run(ResourceEditorLauncher.java:690)
at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35)
at
org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:135)
at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:4140)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3757)
at
org.eclipse.jface.operation.ModalContext$ModalContextThread.block(ModalContext.java:173)
at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:388)
at
org.eclipse.jface.dialogs.ProgressMonitorDialog.run(ProgressMonitorDialog.java:507)
at
org.eclipse.ui.internal.progress.ProgressMonitorJobsDialog.run(ProgressMonitorJobsDialog.java:275)
at
org.eclipse.ui.internal.progress.ProgressManager$5.run(ProgressManager.java:960)
at
org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at
org.eclipse.ui.internal.progress.ProgressManager.busyCursorWhile(ProgressManager.java:995)
at
org.eclipse.ui.internal.progress.ProgressManager.busyCursorWhile(ProgressManager.java:970)
at org.topbraidcomposer.core.io.TBCIO$3.run(TBCIO.java:390)
at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35)
at
org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:135)
at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:4140)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3757)
at
org.eclipse.jface.operation.ModalContext$ModalContextThread.block(ModalContext.java:173)
at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:388)
at org.eclipse.jface.wizard.WizardDialog.run(WizardDialog.java:1029)
at
org.topbraidcomposer.sesame2.remote.create.CreateSesameRemoteWizard.performFinish(CreateSesameRemoteWizard.java:95)
at
org.eclipse.jface.wizard.WizardDialog.finishPressed(WizardDialog.java:827)
at
org.eclipse.jface.wizard.WizardDialog.buttonPressed(WizardDialog.java:432)
at org.eclipse.jface.dialogs.Dialog$2.widgetSelected(Dialog.java:624)
at
org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:240)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
at
org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4165)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3754)
at org.eclipse.jface.window.Window.runEventLoop(Window.java:825)
at org.eclipse.jface.window.Window.open(Window.java:801)
at
org.eclipse.ui.internal.actions.NewWizardShortcutAction.run(NewWizardShortcutAction.java:135)
at org.eclipse.jface.action.Action.runWithEvent(Action.java:498)
at
org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
at
org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
at
org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:411)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1053)
at
org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4165)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3754)
at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2696)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2660)
at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2494)
at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:674)
at
org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at
org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:667)
at
org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at
org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:123)
at
org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at
org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at
org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344)
at
org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577)
at org.eclipse.equinox.launcher.Main.run(Main.java:1410)
at org.eclipse.equinox.launcher.Main.main(Main.java:1386)
Error from Tomcat logs
> Feb 15, 2012 7:38:49 PM org.apache.catalina.core.StandardWrapperValve invoke
> SEVERE: Servlet.service() for servlet [openrdf-http-server] in context
> with path [/openrdf-sesame] threw exception [Request processing failed;
> nested exception is java.lang.ArrayIndexOutOfBoundsException: -1] with
> root cause
> java.lang.ArrayIndexOutOfBoundsException: -1
> at com.ontotext.trree.owlim_ext.c$2.next(Unknown Source)
> at com.ontotext.trree.owlim_ext.Repository$b.next(Unknown Source)
> at com.ontotext.trree.owlim_ext.h$d.if(Unknown Source)
> at com.ontotext.trree.owlim_ext.h$d.a(Unknown Source)
> at com.ontotext.trree.owlim_ext.h$d.next(Unknown Source)
> at
>
info.aduna.iteration.ExceptionConvertingIteration.next(ExceptionConvertingIteration.java:87)
> at
> org.openrdf.repository.RepositoryResult.next(RepositoryResult.java:61)
> at
>
org.openrdf.repository.sail.SailRepositoryConnection.exportStatements(SailRepositoryConnection.java:223)
> at
>
org.openrdf.http.server.repository.statements.ExportStatementsView.render(ExportStatementsView.java:99)
> at
>
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1183)
> at
>
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:902)
> at
>
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:807)
> at
>
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:571)
> at
>
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:501)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
> at
>
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:304)
> at
>
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
> at
>
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
> at
>
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
> at
>
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
> at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:164)
> at
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
> at
> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:929)
> at
>
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
> at
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:405)
> at
> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:279)
> at
>
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:515)
> at
>
org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:302)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
> at java.lang.Thread.run(Unknown Source)
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You received this message because you are subscribed to the Google
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[email protected]
To unsubscribe from this group, send email to
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