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
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
