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wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways
Apache License 2.0
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empty node table and missing names in edge table #84

Closed AlexanderPico closed 5 years ago

AlexanderPico commented 6 years ago

Testing new 3.3.4 jar with 3.7.

Obs: new pathway, but blank Node Table and unnamed rows in Edge Table Exp: full Node and Edge Tables

Threw NPE:

turnOffEvents turnOnEvents turnOffEvents turnOnEvents Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at org.cytoscape.browser.internal.view.BrowserTableModel.setValueAt(BrowserTableModel.java:474) at javax.swing.JTable.setValueAt(JTable.java:2744) at javax.swing.JTable.editingStopped(JTable.java:4729) at javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:141) at javax.swing.AbstractCellEditor.stopCellEditing(AbstractCellEditor.java:85) at javax.swing.plaf.basic.BasicTableUI$Handler.mousePressed(BasicTableUI.java:1010) at javax.swing.plaf.basic.BasicTableUI$MouseInputHandler.mousePressed(BasicTableUI.java:798) at org.cytoscape.browser.internal.view.BrowserTable$ProxyMouseListener.mousePressed(BrowserTable.java:1010) at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) at java.awt.Component.processMouseEvent(Component.java:6536) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6304) at java.awt.Container.processEvent(Container.java:2239) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2297) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4532) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476) at java.awt.Container.dispatchEventImpl(Container.java:2283) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84) at java.awt.EventQueue$4.run(EventQueue.java:733) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:730) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

AlexanderPico commented 6 years ago

Reproduced NPE error after restart. However, within the SAME session, following the NPE, I was able to import-as-network and also import-as-pathway and got full tables!?

AlexanderPico commented 6 years ago

Another oddity... if you select a node, then it shows up in the node table! But unselected (auto mode) or even "show all" mode fail to display any rows.