PathVisio 3.4.0-alpha: Cannot add references to pathways

[alexandra-valeanu]

In PathVisio 3.4.0-alpha, attempting to add references to pathway elements fails.

[egonw]

attempting to add references to pathway elements fails.

@alexandra-valeanu, I guess you also get the following exception?

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at org.pathvisio.core.biopax.PublicationXref.getDb(PublicationXref.java:87)
        at org.pathvisio.gui.dialogs.PublicationXRefDialog.refresh(PublicationXRefDialog.java:98)
        at org.pathvisio.gui.dialogs.PublicationXRefDialog.<init>(PublicationXRefDialog.java:84)
        at org.pathvisio.gui.dialogs.PublicationXRefDialog.<init>(PublicationXRefDialog.java:90)
        at org.pathvisio.gui.CommonActions$AddLiteratureAction.actionPerformed(CommonActions.java:728)
        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
        at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
        at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:882)
        at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:926)
        at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
        at java.awt.Component.processMouseEvent(Component.java:6539)
        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:4535)
        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)