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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