[BioMart Users] marteditor and "Not in Gzip format" exception

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[BioMart Users] marteditor and "Not in Gzip format" exception

Sean Davis
I am new to the biomart server world but have a fair bit of experience using biomart on the client side.  I am working to set up a new biomart webserver.  I have a simple __main table created for testing purposes on a postgresql server running on localhost.  Apache and modperl are configured correctly, I believe.  This is all just background.

Using martj-0.7, I am running marteditor.sh (on mac os).  I can connect to my biomart and with "naive" setup, I see the information that I expect.  The original export appears to work, as I end up with a working martview server running with the default settings for filters and attributes.  However, when I try to make changes or save the configuration, I always see the stack trace shown below and the updates appear to never make it back to the tables on the database server and, hence, do not change in the martview (despite killing the webserver, removing the cached registry, reconfiguring, and then restarting the webserver).

Any suggestions on whether the errors are really the problem with not seeing updates made in marteditor?  If so, is there an explanation and solution?

Thanks,
Sean


Feb 13, 2011 8:21:43 PM org.ensembl.mart.lib.config.DatasetConfig lazyLoad
INFO: LAZYLOAD

Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Could not lazyload datasetconfig Caught IOException during fetch of requested DatasetConfig: Not in GZIP format
        at org.ensembl.mart.lib.config.DatasetConfig.lazyLoad(DatasetConfig.java:1844)
        at org.ensembl.mart.lib.config.DatasetConfig.getImportables(DatasetConfig.java:1009)
        at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.updateConfigToTemplate(DatabaseDatasetConfigUtils.java:2342)
        at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.updateConfigsToTemplate(DatabaseDatasetConfigUtils.java:1722)
        at org.ensembl.mart.editor.DatasetConfigTree.exportTemplate(DatasetConfigTree.java:1586)
        at org.ensembl.mart.editor.DatasetConfigTreeWidget.exportTemplate(DatasetConfigTreeWidget.java:481)
        at org.ensembl.mart.editor.MartEditor.exportTemplate(MartEditor.java:1115)
        at org.ensembl.mart.editor.MartEditor$MenuActionListener.actionPerformed(MartEditor.java:654)
        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
        at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
        at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)
        at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)
        at java.awt.Component.processMouseEvent(Component.java:6352)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
        at java.awt.Component.processEvent(Component.java:6117)
        at java.awt.Container.processEvent(Container.java:2085)
        at java.awt.Component.dispatchEventImpl(Component.java:4714)
        at java.awt.Container.dispatchEventImpl(Container.java:2143)
        at java.awt.Component.dispatchEvent(Component.java:4544)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
        at java.awt.Container.dispatchEventImpl(Container.java:2129)
        at java.awt.Window.dispatchEventImpl(Window.java:2478)
        at java.awt.Component.dispatchEvent(Component.java:4544)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: org.ensembl.mart.lib.config.ConfigurationException: Caught IOException during fetch of requested DatasetConfig: Not in GZIP format
        at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.getDatasetConfigDocumentByDatasetID(DatabaseDatasetConfigUtils.java:3823)
        at org.ensembl.mart.lib.config.DatabaseDSConfigAdaptor.lazyLoadWithDatabase(DatabaseDSConfigAdaptor.java:291)
        at org.ensembl.mart.lib.config.DatabaseDSConfigAdaptor.lazyLoad(DatabaseDSConfigAdaptor.java:324)
        at org.ensembl.mart.lib.config.DatasetConfig.lazyLoad(DatasetConfig.java:1840)
        ... 34 more
Caused by: java.io.IOException: Not in GZIP format
        at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:137)
        at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:58)
        at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:68)
        at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.getDatasetConfigDocumentByDatasetID(DatabaseDatasetConfigUtils.java:3813)
        ... 37 more

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Re: [BioMart Users] marteditor and "Not in Gzip format" exception

Syed Haider
Hi Sean,

Could you please try File->Save All (this will save your xmls to file
system) and then File->UpLoad All (multi-select all the files that you
saved). Now try export and see if it helps. If that doesnt help either,
send me your xmls and we have a look on our side.

Also, you can try BioMart 0.8 release candidate 4
(http://www.biomart.org/rc4_documentation.pdf) which is an all new java
based BioMart.

Syed

On 14/02/2011 01:36, Sean Davis wrote:

> I am new to the biomart server world but have a fair bit of experience using biomart on the client side.  I am working to set up a new biomart webserver.  I have a simple __main table created for testing purposes on a postgresql server running on localhost.  Apache and modperl are configured correctly, I believe.  This is all just background.
>
> Using martj-0.7, I am running marteditor.sh (on mac os).  I can connect to my biomart and with "naive" setup, I see the information that I expect.  The original export appears to work, as I end up with a working martview server running with the default settings for filters and attributes.  However, when I try to make changes or save the configuration, I always see the stack trace shown below and the updates appear to never make it back to the tables on the database server and, hence, do not change in the martview (despite killing the webserver, removing the cached registry, reconfiguring, and then restarting the webserver).
>
> Any suggestions on whether the errors are really the problem with not seeing updates made in marteditor?  If so, is there an explanation and solution?
>
> Thanks,
> Sean
>
>
> Feb 13, 2011 8:21:43 PM org.ensembl.mart.lib.config.DatasetConfig lazyLoad
> INFO: LAZYLOAD
>
> Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Could not lazyload datasetconfig Caught IOException during fetch of requested DatasetConfig: Not in GZIP format
>          at org.ensembl.mart.lib.config.DatasetConfig.lazyLoad(DatasetConfig.java:1844)
>          at org.ensembl.mart.lib.config.DatasetConfig.getImportables(DatasetConfig.java:1009)
>          at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.updateConfigToTemplate(DatabaseDatasetConfigUtils.java:2342)
>          at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.updateConfigsToTemplate(DatabaseDatasetConfigUtils.java:1722)
>          at org.ensembl.mart.editor.DatasetConfigTree.exportTemplate(DatasetConfigTree.java:1586)
>          at org.ensembl.mart.editor.DatasetConfigTreeWidget.exportTemplate(DatasetConfigTreeWidget.java:481)
>          at org.ensembl.mart.editor.MartEditor.exportTemplate(MartEditor.java:1115)
>          at org.ensembl.mart.editor.MartEditor$MenuActionListener.actionPerformed(MartEditor.java:654)
>          at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
>          at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
>          at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
>          at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
>          at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
>          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)
>          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)
>          at java.awt.Component.processMouseEvent(Component.java:6352)
>          at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
>          at java.awt.Component.processEvent(Component.java:6117)
>          at java.awt.Container.processEvent(Container.java:2085)
>          at java.awt.Component.dispatchEventImpl(Component.java:4714)
>          at java.awt.Container.dispatchEventImpl(Container.java:2143)
>          at java.awt.Component.dispatchEvent(Component.java:4544)
>          at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
>          at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
>          at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
>          at java.awt.Container.dispatchEventImpl(Container.java:2129)
>          at java.awt.Window.dispatchEventImpl(Window.java:2478)
>          at java.awt.Component.dispatchEvent(Component.java:4544)
>          at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
>          at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
>          at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
>          at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
>          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
>          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
>          at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Caused by: org.ensembl.mart.lib.config.ConfigurationException: Caught IOException during fetch of requested DatasetConfig: Not in GZIP format
>          at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.getDatasetConfigDocumentByDatasetID(DatabaseDatasetConfigUtils.java:3823)
>          at org.ensembl.mart.lib.config.DatabaseDSConfigAdaptor.lazyLoadWithDatabase(DatabaseDSConfigAdaptor.java:291)
>          at org.ensembl.mart.lib.config.DatabaseDSConfigAdaptor.lazyLoad(DatabaseDSConfigAdaptor.java:324)
>          at org.ensembl.mart.lib.config.DatasetConfig.lazyLoad(DatasetConfig.java:1840)
>          ... 34 more
> Caused by: java.io.IOException: Not in GZIP format
>          at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:137)
>          at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:58)
>          at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:68)
>          at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.getDatasetConfigDocumentByDatasetID(DatabaseDatasetConfigUtils.java:3813)
>          ... 37 more
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Re: [BioMart Users] marteditor and "Not in Gzip format" exception

Sean Davis


On Sun, Feb 13, 2011 at 8:53 PM, Syed Haider <[hidden email]> wrote:
Hi Sean,

Could you please try File->Save All (this will save your xmls to file
system) and then File->UpLoad All (multi-select all the files that you
saved). Now try export and see if it helps. If that doesnt help either,
send me your xmls and we have a look on our side.


Hi, Syed.  I tried going that route.  Even Save All results in the error.  I'll try again on another machine in the next day or so and report back.
 
Also, you can try BioMart 0.8 release candidate 4
(http://www.biomart.org/rc4_documentation.pdf) which is an all new java
based BioMart.


I have given that a try.  it looks quite slick and works pretty well for me, at least after 30 minutes of playing with it--I think I'll probably stick with it for now.  

Thanks,
Sean

 
Syed

On 14/02/2011 01:36, Sean Davis wrote:
> I am new to the biomart server world but have a fair bit of experience using biomart on the client side.  I am working to set up a new biomart webserver.  I have a simple __main table created for testing purposes on a postgresql server running on localhost.  Apache and modperl are configured correctly, I believe.  This is all just background.
>
> Using martj-0.7, I am running marteditor.sh (on mac os).  I can connect to my biomart and with "naive" setup, I see the information that I expect.  The original export appears to work, as I end up with a working martview server running with the default settings for filters and attributes.  However, when I try to make changes or save the configuration, I always see the stack trace shown below and the updates appear to never make it back to the tables on the database server and, hence, do not change in the martview (despite killing the webserver, removing the cached registry, reconfiguring, and then restarting the webserver).
>
> Any suggestions on whether the errors are really the problem with not seeing updates made in marteditor?  If so, is there an explanation and solution?
>
> Thanks,
> Sean
>
>
> Feb 13, 2011 8:21:43 PM org.ensembl.mart.lib.config.DatasetConfig lazyLoad
> INFO: LAZYLOAD
>
> Exception in thread "AWT-EventQueue-0" java.lang.RuntimeException: Could not lazyload datasetconfig Caught IOException during fetch of requested DatasetConfig: Not in GZIP format
>          at org.ensembl.mart.lib.config.DatasetConfig.lazyLoad(DatasetConfig.java:1844)
>          at org.ensembl.mart.lib.config.DatasetConfig.getImportables(DatasetConfig.java:1009)
>          at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.updateConfigToTemplate(DatabaseDatasetConfigUtils.java:2342)
>          at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.updateConfigsToTemplate(DatabaseDatasetConfigUtils.java:1722)
>          at org.ensembl.mart.editor.DatasetConfigTree.exportTemplate(DatasetConfigTree.java:1586)
>          at org.ensembl.mart.editor.DatasetConfigTreeWidget.exportTemplate(DatasetConfigTreeWidget.java:481)
>          at org.ensembl.mart.editor.MartEditor.exportTemplate(MartEditor.java:1115)
>          at org.ensembl.mart.editor.MartEditor$MenuActionListener.actionPerformed(MartEditor.java:654)
>          at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
>          at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
>          at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
>          at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
>          at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
>          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)
>          at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)
>          at java.awt.Component.processMouseEvent(Component.java:6352)
>          at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
>          at java.awt.Component.processEvent(Component.java:6117)
>          at java.awt.Container.processEvent(Container.java:2085)
>          at java.awt.Component.dispatchEventImpl(Component.java:4714)
>          at java.awt.Container.dispatchEventImpl(Container.java:2143)
>          at java.awt.Component.dispatchEvent(Component.java:4544)
>          at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
>          at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
>          at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
>          at java.awt.Container.dispatchEventImpl(Container.java:2129)
>          at java.awt.Window.dispatchEventImpl(Window.java:2478)
>          at java.awt.Component.dispatchEvent(Component.java:4544)
>          at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
>          at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
>          at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
>          at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
>          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
>          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
>          at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> Caused by: org.ensembl.mart.lib.config.ConfigurationException: Caught IOException during fetch of requested DatasetConfig: Not in GZIP format
>          at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.getDatasetConfigDocumentByDatasetID(DatabaseDatasetConfigUtils.java:3823)
>          at org.ensembl.mart.lib.config.DatabaseDSConfigAdaptor.lazyLoadWithDatabase(DatabaseDSConfigAdaptor.java:291)
>          at org.ensembl.mart.lib.config.DatabaseDSConfigAdaptor.lazyLoad(DatabaseDSConfigAdaptor.java:324)
>          at org.ensembl.mart.lib.config.DatasetConfig.lazyLoad(DatasetConfig.java:1840)
>          ... 34 more
> Caused by: java.io.IOException: Not in GZIP format
>          at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:137)
>          at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:58)
>          at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:68)
>          at org.ensembl.mart.lib.config.DatabaseDatasetConfigUtils.getDatasetConfigDocumentByDatasetID(DatabaseDatasetConfigUtils.java:3813)
>          ... 37 more


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