Hi Vincent, Great news. All you say is correct :) Junjun cc'ed here will be able to point you to the Mloader docs. Yong; can you help Vincent with the "materialize" exception please?
a Arek Kasprzyk Director, Bioinformatics Operations and Principal Investigator Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8559 Toll-free: 1-866-678-6427 www.oicr.on.ca Administrative Assistant: [email protected] This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. From: Vincent Le Texier <[email protected]<mailto:[email protected]>> Date: Fri, 25 Mar 2011 10:05:34 -0400 To: Arek Kasprzyk <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] AWT-EventQueue error when doing Materialize Hello Arek, Ok so this does not apply for the ICGC deployment. I am currently reading the documentation since we will have some somatic mutations data to share (I think It will come after June, so not for the next release). anyway, I have installed and configured biomart (http://lumiere.lyon.fnclcc.fr/ICGC/), not finished yet, but it will be the French ICGC data portal. If I remember correctly since Brisbane, you can publish the data through a local database thanks to a martloader script. Then you can use MartConfigurator to register your site to the Biomart Central registry. am I right ? so how do I create this local MySQL database to load/store/update and share our data ? This is just what I want to do right now. Thanks Vincent. Le 3/25/11 2:34 PM, Arek Kasprzyk a écrit : Vincent: Before someone gets back to you with help I just want to double check that you are not doing this for the ICGC deployment. There is dedicated install section in rc5 for the icgc install and the process does not require materializing anything a Arek Kasprzyk Director, Bioinformatics Operations and Principal Investigator Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8559 Toll-free: 1-866-678-6427 www.oicr.on.ca<http://www.oicr.on.ca> Administrative Assistant: [email protected]<mailto:[email protected]> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. From: Vincent Le Texier <[email protected]<mailto:[email protected]>> Date: Fri, 25 Mar 2011 09:28:13 -0400 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [BioMart Users] AWT-EventQueue error when doing Materialize Hello, I have just deployed the rc5 and I have a problem doing "Materialize" on a data source. I get the following error : Any idea of the problem ? Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at org.biomart.configurator.view.gui.dialogs.SaveDDLDialog$4.itemStateChanged(SaveDDLDialog.java:274) at javax.swing.JComboBox.fireItemStateChanged(JComboBox.java:1224) at javax.swing.JComboBox.selectedItemChanged(JComboBox.java:1272) at javax.swing.JComboBox.contentsChanged(JComboBox.java:1328) at javax.swing.AbstractListModel.fireContentsChanged(AbstractListModel.java:117) at javax.swing.DefaultComboBoxModel.setSelectedItem(DefaultComboBoxModel.java:105) at javax.swing.JComboBox.setSelectedItem(JComboBox.java:576) at org.biomart.configurator.view.gui.dialogs.SaveDDLDialog.<init>(SaveDDLDialog.java:388) at org.biomart.configurator.view.menu.ContextMenuConstructor.actionPerformed(ContextMenuConstructor.java:602) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2012) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2335) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:404) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:374) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1688) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1732) at java.awt.Component.processMouseEvent(Component.java:6108) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:5873) at java.awt.Container.processEvent(Container.java:2105) at java.awt.Component.dispatchEventImpl(Component.java:4469) at java.awt.Container.dispatchEventImpl(Container.java:2163) at java.awt.Component.dispatchEvent(Component.java:4295) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4461) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4125) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4055) at java.awt.Container.dispatchEventImpl(Container.java:2149) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4295) at java.awt.EventQueue.dispatchEvent(EventQueue.java:604) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177) at java.awt.EventDispatchThread.run(EventDispatchThread.java:138) -- Vincent Le Texier Senior Software Engineer Synergie Lyon Cancer Leon Berard Center, Cheney C 28, rue Laennec 69373 LYON Cedex 08 +33 4 26 55 67 85 [email protected]<mailto:[email protected]> -- Vincent Le Texier Senior Software Engineer Synergie Lyon Cancer Leon Berard Center, Cheney C 28, rue Laennec 69373 LYON Cedex 08 +33 4 26 55 67 85 [email protected]<mailto:[email protected]>
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