No response for AttributeSearch give PV error #40
Description
Issue with searching terms from PV/webservice
@egonw
While using the webservice from PathVisio, we notified that the search term 'glucose 6' and 'adenosine triphosphate' gives an error in PV (3.3.0) (see printscreen below).
The error log gave the following message:
ArrayIndexOutOfBoundsException: 1
[...]
at org.bridgedb.webservice.bridgerest.BridgeRest.freeAttributeSearch(BridgeRest.java:437)
Testing the same search terms in the BridgeDb webservice gave a response (200); however the response was empty.
Not sure if the issues is causes by the space in the search term, or that there is no response at all.
The ATP item in Wikidata Q80863 has the label with space in it, and should be searchable I believe.
Printscreens and detailed error log:
Error: Error while searching
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 1: java.lang.ArrayIndexOutOfBoundsException: 1
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 1
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at javax.swing.SwingWorker.get(SwingWorker.java:602)
at org.pathvisio.gui.dialogs.DataNodeDialog$1.done(Unknown Source)
at javax.swing.SwingWorker$5.run(SwingWorker.java:737)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832)
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842)
at javax.swing.Timer.fireActionPerformed(Timer.java:313)
at javax.swing.Timer$DoPostEvent.run(Timer.java:245)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
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.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233)
at java.awt.Dialog.show(Dialog.java:1084)
at java.awt.Component.show(Component.java:1671)
at java.awt.Component.setVisible(Component.java:1623)
at java.awt.Window.setVisible(Window.java:1014)
at java.awt.Dialog.setVisible(Dialog.java:1005)
at org.pathvisio.gui.dialogs.DataNodeDialog.search(Unknown Source)
at org.pathvisio.gui.dialogs.DataNodeDialog.access$200(Unknown Source)
at org.pathvisio.gui.dialogs.DataNodeDialog$3.actionPerformed(Unknown Source)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:262)
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.pumpEventsForFilter(EventDispatchThread.java:109)
at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233)
at java.awt.Dialog.show(Dialog.java:1084)
at java.awt.Component.show(Component.java:1671)
at java.awt.Component.setVisible(Component.java:1623)
at java.awt.Window.setVisible(Window.java:1014)
at java.awt.Dialog.setVisible(Dialog.java:1005)
at org.pathvisio.gui.MainPanel.vPathwayEvent(Unknown Source)
at org.pathvisio.core.view.VPathway.fireVPathwayEvent(Unknown Source)
at org.pathvisio.core.view.VPathway.mouseDoubleClick(Unknown Source)
at org.pathvisio.gui.view.VPathwaySwing.mouseClicked(Unknown Source)
at java.awt.Component.processMouseEvent(Component.java:6542)
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:4544)
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)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1
at org.bridgedb.webservice.bridgerest.BridgeRest.freeAttributeSearch(BridgeRest.java:437)
at org.bridgedb.IDMapperStack.freeAttributeSearch(IDMapperStack.java:427)
at org.pathvisio.gui.dialogs.DataNodeDialog$1.doInBackground(Unknown Source)
at org.pathvisio.gui.dialogs.DataNodeDialog$1.doInBackground(Unknown Source)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)