[biomart-users] Error in mart editor config import

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[biomart-users] Error in mart editor config import

CancerBio
Hi,

After a small change on the data included in our test server and biomart reload, I can no longer "import" the server configuration for editing on mart editor (using BioMart 0.7 and martj-0.7 on Linux). I would appreciate some help recovering from the error without having to reload the database schema:


Starting MartEditor please wait .... 

getting driver com.mysql.jdbc.Driver

java.lang.NullPointerException

at org.ensembl.mart.lib.config.DatasetConfigXMLUtils.loadDatasetConfigWithDocument(DatasetConfigXMLUtils.java:229)

at org.ensembl.mart.editor.DatasetConfigTreeWidget.<init>(DatasetConfigTreeWidget.java:162)

at org.ensembl.mart.editor.MartEditor.importTemplateConfig(MartEditor.java:947)

at org.ensembl.mart.editor.MartEditor$MenuActionListener.actionPerformed(MartEditor.java:650)

at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)

at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)

at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)

at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)

at javax.swing.AbstractButton.doClick(AbstractButton.java:357)

at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)

at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)

at java.awt.Component.processMouseEvent(Component.java:6297)

at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)

at java.awt.Component.processEvent(Component.java:6062)

at java.awt.Container.processEvent(Container.java:2039)

at java.awt.Component.dispatchEventImpl(Component.java:4660)

at java.awt.Container.dispatchEventImpl(Container.java:2097)

at java.awt.Component.dispatchEvent(Component.java:4488)

at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4575)

at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4236)

at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4166)

at java.awt.Container.dispatchEventImpl(Container.java:2083)

at java.awt.Window.dispatchEventImpl(Window.java:2489)

at java.awt.Component.dispatchEvent(Component.java:4488)

at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:668)

at java.awt.EventQueue.access$400(EventQueue.java:81)

at java.awt.EventQueue$2.run(EventQueue.java:627)

at java.awt.EventQueue$2.run(EventQueue.java:625)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)

at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)

at java.awt.EventQueue$3.run(EventQueue.java:641)

at java.awt.EventQueue$3.run(EventQueue.java:639)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:638)

at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)

at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

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Re: [biomart-users] Error in mart editor config import

Arek Kasprzyk
Hi

could you send us a little more details what exactly was changed in your database. It is difficult to help you just based on this error message

a.

On 29 September 2015 at 12:57, CancerBio <[hidden email]> wrote:
Hi,

After a small change on the data included in our test server and biomart reload, I can no longer "import" the server configuration for editing on mart editor (using BioMart 0.7 and martj-0.7 on Linux). I would appreciate some help recovering from the error without having to reload the database schema:


Starting MartEditor please wait .... 

getting driver com.mysql.jdbc.Driver

java.lang.NullPointerException

at org.ensembl.mart.lib.config.DatasetConfigXMLUtils.loadDatasetConfigWithDocument(DatasetConfigXMLUtils.java:229)

at org.ensembl.mart.editor.DatasetConfigTreeWidget.<init>(DatasetConfigTreeWidget.java:162)

at org.ensembl.mart.editor.MartEditor.importTemplateConfig(MartEditor.java:947)

at org.ensembl.mart.editor.MartEditor$MenuActionListener.actionPerformed(MartEditor.java:650)

at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)

at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)

at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)

at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)

at javax.swing.AbstractButton.doClick(AbstractButton.java:357)

at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)

at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)

at java.awt.Component.processMouseEvent(Component.java:6297)

at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)

at java.awt.Component.processEvent(Component.java:6062)

at java.awt.Container.processEvent(Container.java:2039)

at java.awt.Component.dispatchEventImpl(Component.java:4660)

at java.awt.Container.dispatchEventImpl(Container.java:2097)

at java.awt.Component.dispatchEvent(Component.java:4488)

at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4575)

at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4236)

at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4166)

at java.awt.Container.dispatchEventImpl(Container.java:2083)

at java.awt.Window.dispatchEventImpl(Window.java:2489)

at java.awt.Component.dispatchEvent(Component.java:4488)

at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:668)

at java.awt.EventQueue.access$400(EventQueue.java:81)

at java.awt.EventQueue$2.run(EventQueue.java:627)

at java.awt.EventQueue$2.run(EventQueue.java:625)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)

at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)

at java.awt.EventQueue$3.run(EventQueue.java:641)

at java.awt.EventQueue$3.run(EventQueue.java:639)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:638)

at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)

at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

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