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Read database list error, INNODB problem?
Posted by: Ugo Bellavance
Date: March 07, 2012 11:38AM


I've filled the filesystem where resides my mysql database a few days ago and all databases seem to have been OK with that (once I freed space) except one, which is INNODB.

This database is the database backend for the Talend Administration Console. Talend is an ETL product that is quite complex and the MySQL database is the backend for their console, which work fine, except when we want to play with ETL jobs. I won't go into details unless if I'm asked to because I think this may be a problem with MySQL. The DB is on our central MySQL server and Talend is installed on another server (both VMWare VMs, same network, same physical host).

Here are the two errors that I got at first:

Unexpected exception on: org.talend.administrator.common.exception.DBException: ???Cannot flush and commit transaction.???

Lock wait timeout exceeded; try restarting transaction

Since then I've backed up the DB, restored it but got this error once in a while. I didn't get this error since yesterday, noon, but here is the reason why I think I may have screwed something with my MySQL server:

When I use DBeaver to access my DBs (no error with MySQL Workbench), I get java.lang.NullPointerException (see full log at the bottom of this post)

One mistake that I did is to create a copy of the DB, then delete it directly on the filesystem. I guess by doing that, the information_scheme didn't get updated.

I did a check table and analyse table on all the tables on all databases on this server. But I can't do a repair on InnoDB tables because InnoDB doesn't support that.

It there a way I could perform a health check of my DBs?

Thanks in advance.

at org.jkiss.dbeaver.model.impl.AbstractObjectCache.getCachedObject(
at org.jkiss.dbeaver.ext.mysql.model.MySQLDataSource.getCatalog(
at org.jkiss.dbeaver.ext.mysql.model.MySQLDataSource.getSelectedObject(
at org.jkiss.dbeaver.ext.mysql.model.MySQLDataSource.getSelectedObject(
at org.jkiss.dbeaver.ui.views.navigator.database.DatabaseNavigatorLabelProvider.isDefaultElement(
at org.jkiss.dbeaver.ui.views.navigator.database.DatabaseNavigatorLabelProvider.getFont(
at org.eclipse.jface.viewers.WrappedViewerLabelProvider.getFont(
at org.eclipse.jface.viewers.WrappedViewerLabelProvider.update(
at org.eclipse.jface.viewers.ViewerColumn.refresh(
at org.eclipse.jface.viewers.AbstractTreeViewer.doUpdateItem(
at org.eclipse.jface.viewers.AbstractTreeViewer$
at org.eclipse.ui.internal.JFaceUtil$
at org.eclipse.jface.viewers.AbstractTreeViewer.doUpdateItem(
at org.eclipse.jface.viewers.AbstractTreeViewer.internalRefresh(
at org.eclipse.jface.viewers.AbstractTreeViewer.internalRefresh(
at org.eclipse.jface.viewers.AbstractTreeViewer.internalRefresh(
at org.eclipse.jface.viewers.AbstractTreeViewer.createAddedElements(
at org.eclipse.jface.viewers.AbstractTreeViewer.internalAdd(
at org.eclipse.jface.viewers.TreeViewer.internalAdd(
at org.eclipse.jface.viewers.AbstractTreeViewer.add(
at org.jkiss.dbeaver.ui.views.navigator.database.load.TreeLoadVisualizer.completeLoading(
at org.jkiss.dbeaver.ui.views.navigator.database.load.TreeLoadVisualizer.completeLoading(
at org.eclipse.ui.internal.UILockListener.doPendingWork(
at org.eclipse.ui.internal.UISynchronizer$
at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(
at org.eclipse.swt.widgets.Display.runAsyncMessages(
at org.eclipse.swt.widgets.Display.readAndDispatch(
at org.eclipse.ui.internal.Workbench.runEventLoop(
at org.eclipse.ui.internal.Workbench.runUI(
at org.eclipse.ui.internal.Workbench.access$4(
at org.eclipse.ui.internal.Workbench$
at org.eclipse.core.databinding.observable.Realm.runWithDefault(
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(
at org.jkiss.dbeaver.core.DBeaverApplication.start(
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(
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(
at org.eclipse.equinox.launcher.Main.basicRun(

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Read database list error, INNODB problem?
March 07, 2012 11:38AM

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