On Sun, Feb 13, 2011 at 8:53 PM, Syed Haider <[email protected]> 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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