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BaderLab / EnrichmentMapApp

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
http://apps.cytoscape.org/apps/enrichmentmap
GNU Lesser General Public License v2.1
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Unable to create Enrichment Map: Internal Server Error - Failed: empty String #381

Closed mjrich79 closed 4 years ago

mjrich79 commented 5 years ago

I am trying to build a map using GSEA and the plugin. I am able to get through the workflow fine up until I want to create a map. I am getting the same error whether I try and launch from EnrichmentMap in Cytoscape or from GSEA.

some additional info in the window.

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at org.gsea_msigdb.gsea/edu.mit.broad.cytoscape.view.EnrichmentMapParameterPanel.selectJaccardOrOverlapActionPerformed(EnrichmentMapParameterPanel.java:462) at org.gsea_msigdb.gsea/edu.mit.broad.cytoscape.view.EnrichmentMapParameterPanel.access$100(EnrichmentMapParameterPanel.java:54) at org.gsea_msigdb.gsea/edu.mit.broad.cytoscape.view.EnrichmentMapParameterPanel$2.actionPerformed(EnrichmentMapParameterPanel.java:225) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at java.desktop/javax.swing.JToggleButton$ToggleButtonModel.setPressed(Unknown Source) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) at looks@2.0.4/com.jgoodies.looks.plastic.ActiveBasicButtonListener.mouseReleased(ActiveBasicButtonListener.java:69) at java.desktop/java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) at java.desktop/java.awt.Component.processMouseEvent(Unknown Source) at java.desktop/javax.swing.JComponent.processMouseEvent(Unknown Source) at java.desktop/java.awt.Component.processEvent(Unknown Source) at java.desktop/java.awt.Container.processEvent(Unknown Source) at java.desktop/java.awt.Component.dispatchEventImpl(Unknown Source) at java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source) at java.desktop/java.awt.Component.dispatchEvent(Unknown Source) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source) at java.desktop/java.awt.Window.dispatchEventImpl(Unknown Source) at java.desktop/java.awt.Component.dispatchEvent(Unknown Source) at java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.desktop/java.awt.EventQueue$4.run(Unknown Source) at java.desktop/java.awt.EventQueue$4.run(Unknown Source) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.desktop/java.awt.EventQueue$5.run(Unknown Source) at java.desktop/java.awt.EventQueue$5.run(Unknown Source) at java.base/java.security.AccessController.doPrivileged(Native Method) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.desktop/java.awt.EventDispatchThread.run(Unknown Source)

risserlin commented 5 years ago

What version of cytoscape and enrichment map are you using? Also, are you on Windows, Mac or linux?
It looks like it might not be able to even open the EM panel. Are you able to enter all your GSEA results files into the interface but when you push on build it fails with the above error message?

mikekucera commented 4 years ago

The stack trace is from GSEA desktop not from EnrichmentMap.