[BioMart Users] AWT-EventQueue error when doing Materialize

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[BioMart Users] AWT-EventQueue error when doing Materialize

Vincent Le Texier
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
[hidden email]

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Re: [BioMart Users] AWT-EventQueue error when doing Materialize

Arek Kasprzyk-2
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


Administrative Assistant: [hidden email]

 

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 <[hidden email]>
Date: Fri, 25 Mar 2011 09:28:13 -0400
To: "[hidden email]" <[hidden email]>
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
[hidden email]

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Re: [BioMart Users] AWT-EventQueue error when doing Materialize

Arek Kasprzyk-2
In reply to this post by Vincent Le Texier
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: [hidden email]

 

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 <[hidden email]>
Date: Fri, 25 Mar 2011 10:05:34 -0400
To: Arek Kasprzyk <[hidden email]>
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


Administrative Assistant: [hidden email]

 

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 <[hidden email]>
Date: Fri, 25 Mar 2011 09:28:13 -0400
To: "[hidden email]" <[hidden email]>
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
[hidden email]


-- 
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
[hidden email]

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Users mailing list
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Re: [BioMart Users] AWT-EventQueue error when doing Materialize

Yong Liang
In reply to this post by Vincent Le Texier
Hi Vincent,

I could not reproduce the problem on my side. Could you give me more detail
about how you got the error?

Thanks,

Yong


On 11-03-25 9:28 AM, "Vincent Le Texier" <[hidden email]> wrote:

>    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(Sav
> eDDLDialog.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.j
> ava:388)
>      at
> org.biomart.configurator.view.menu.ContextMenuConstructor.actionPerformed(Cont
> extMenuConstructor.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.j
> ava: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:2
> 75)
>      at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
>      at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:1
> 90)
>      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
>      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)
>  
>  

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[BioMart Users] ERROR: Can't call method "getConfigurationTree"

nndegwa
In reply to this post by Arek Kasprzyk-2
Hi,
I am experiencing some problems with BioMart v07, where my previously
working queries are now throwing this error which doesn't seem to have
any useful Google search result clues to work with: Any ideas?
Many thanks,
Nelson

ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method
"getConfigurationTree" on an undefined value at
/automount/nas17b_vol-vol_homes-homes/nndegwa/soft/biomart/biomart-perl/lib/BioMart/Web.pm
line 786.

If you repeatedly get directed to this error page, there may be a
problem with your current session parameters. To clear your session and
start with a clean slate, please click the *New* button below.

Stacktrace:
Exception::Class::Base::new
/automount/nas17b_vol-vol_homes-homes/nndegwa/soft/biomart/biomart-perl/cgi-bin/martview:102
ModPerl::ROOT::ModPerl::Registry::automount_nas17b_vol_2dvol_homes_2dhomes_nndegwa_soft_biomart_biomart_2dperl_cgi_2dbin_martview::handler
/homes/nndegwa/soft/perl/5.10.1/lib/site_perl/5.10.1/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
(eval)
/homes/nndegwa/soft/perl/5.10.1/lib/site_perl/5.10.1/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run
/homes/nndegwa/soft/perl/5.10.1/lib/site_perl/5.10.1/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler
/homes/nndegwa/soft/perl/5.10.1/lib/site_perl/5.10.1/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0


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Re: [BioMart Users] ERROR: Can't call method "getConfigurationTree"

Joachim Baran-2
Hi Nelson!

On 11-03-28 8:29 AM, "Nelson Ndegwa" <[hidden email]> wrote:
>ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method
>"getConfigurationTree" on an undefined value at
>/automount/nas17b_vol-vol_homes-homes/nndegwa/soft/biomart/biomart-perl/li
>b/BioMart/Web.pm
>line 786.
  Having had a look into the code, it seems that the dataset cannot be
fetched anymore.

  Can you please verify whether your BioMart database/tables or
configuration might have changed? Seeing that you are working on a shared
system, someone else might have changed something without your knowledge.
If you are editing configuration files in your home directory on one
machine, but execute the server on a different machine, you should keep in
mind that the NAS might not immediately propagate the filesystem changes
instantly (depending on how the NAS is mounted).

Joachim

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Re: [BioMart Users] AWT-EventQueue error when doing Materialize

Junjun Zhang
In reply to this post by Arek Kasprzyk-2
Re: [BioMart Users] AWT-EventQueue error when doing Materialize Hi Vincent,

Please get the ICGC data submission guide at http://dcc.icgc.org/docs/ICGC_data_submission_manual.pdf. There are sections on how to download martloader and how run it to process ICGC data sets.

Let me know if you have any questions.

Cheers,
Junjun


On 11-03-25 9:16 AM, "Arek Kasprzyk" <Arek.Kasprzyk@...> wrote:

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: Natasha.Lander@...

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 <letexier@...>
Date: Fri, 25 Mar 2011 10:05:34 -0400
To: Arek Kasprzyk <arek.kasprzyk@...>
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: Natasha.Lander@...



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 <letexier@...>
 Date: Fri, 25 Mar 2011 09:28:13 -0400
 To: "users@..." <users@...>
 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)
 
 

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Re: [BioMart Users] ERROR: Can't call method "getConfigurationTree"

nndegwa
In reply to this post by Joachim Baran-2
Hi Joachim,
Thanks, this issue is now solved. We are using in-house canned queries
for federation to a different mart which it turns out they had updated
their mart and renamed their datasets, sadly the log files weren't
showing any clues to this effect.
Many thanks,
Nelson

Joachim Baran wrote:

> Hi Nelson!
>
> On 11-03-28 8:29 AM, "Nelson Ndegwa" <[hidden email]> wrote:
>  
>> ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method
>> "getConfigurationTree" on an undefined value at
>> /automount/nas17b_vol-vol_homes-homes/nndegwa/soft/biomart/biomart-perl/li
>> b/BioMart/Web.pm
>> line 786.
>>    
>   Having had a look into the code, it seems that the dataset cannot be
> fetched anymore.
>
>   Can you please verify whether your BioMart database/tables or
> configuration might have changed? Seeing that you are working on a shared
> system, someone else might have changed something without your knowledge.
> If you are editing configuration files in your home directory on one
> machine, but execute the server on a different machine, you should keep in
> mind that the NAS might not immediately propagate the filesystem changes
> instantly (depending on how the NAS is mounted).
>
> Joachim
>
>  

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