Details
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Type: Bug
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Status: Closed
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Priority: Blocker
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Resolution: Fixed
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Affects Version/s: 2.8
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Fix Version/s: 2.8.1
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Component/s: Dev and Dep, JWS2
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Labels:None
Description
(Reported by Roman Pekhletski at utoronto via jabaws-discuss-owner)
Symptoms: Jalview is unable to access locally installed JABAWS servers, or the public JABAWS servers.
Caused by an incompatibility between the java VM shipped with InstallAnywhere and the JABAWS code.
Exceptions raised (partial dump from jalview console):
Dec 17, 2012 3:53:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Checking service MafftWS
Testing alignment with default parameters:
Querying job status...FAILED
Exception while waiting for results. Exception details are below:
object is not an instance of declaring class
java.lang.IllegalArgumentException: object is not an instance of declaring class
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.xml.internal.ws.client.EndpointIFInvocationHandler.invoke(Unknown Source)
at $Proxy17.getJobStatus(Unknown Source)
at compbio.ws.client.WSTester.testDefaultAlignment(Unknown Source)
at compbio.ws.client.WSTester.testMsaWS(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:684)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:486)
at jalview.gui.WsPreferences.editWsUrl_actionPerformed(WsPreferences.java:275)
at jalview.jbgui.GWsPreferences$16.mouseClicked(GWsPreferences.java:305)
at java.awt.AWTEventMulticaster.mouseClicked(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Componentjava.lang.ClassCastException: $Proxy17 cannot be cast to java.io.Closeable
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:684)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:486)
at jalview.gui.WsPreferences.editWsUrl_actionPerformed(WsPreferences.java:275)
at jalview.jbgui.GWsPreferences$16.mouseClicked(GWsPreferences.java:305)
at java.awt.AWTEventMulticaster.mouseClicked(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java..dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
<ServiceName> is not provided checking all known services...
Dec 17, 2012 3:54:02 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Checking service MafftWS
Testing alignment with default parameters:
Querying job status...FAILED
Exception while waiting for results. Exception details are below:
object is not an instance of declaring class
java.lang.IllegalArgumentException: object is not an instance of declaring class
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.xml.internal.ws.client.EndpointIFInvocationHandler.invoke(Unknown Source)
at $Proxy17.getJobStatus(Unknown Source)
at compbio.ws.client.WSTester.testDefaultAlignment(Unknown Source)
at compbio.ws.client.WSTester.testMsaWS(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:684)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:486)
at jalview.gui.WsPreferences.editWsUrl_actionPerformed(WsPreferences.java:275)
at jalview.jbgui.GWsPreferences$9.actionPerformed(GWsPreferences.java:224)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvjava.lang.ClassCastException: $Proxy17 cannot be cast to java.io.Closeable
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:684)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:486)
at jalview.gui.WsPreferences.editWsUrl_actionPerformed(WsPreferences.java:275)
at jalview.jbgui.GWsPreferences$9.actionPerformed(GWsPreferences.java:224)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
t.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Symptoms: Jalview is unable to access locally installed JABAWS servers, or the public JABAWS servers.
Caused by an incompatibility between the java VM shipped with InstallAnywhere and the JABAWS code.
Exceptions raised (partial dump from jalview console):
Dec 17, 2012 3:53:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Checking service MafftWS
Testing alignment with default parameters:
Querying job status...FAILED
Exception while waiting for results. Exception details are below:
object is not an instance of declaring class
java.lang.IllegalArgumentException: object is not an instance of declaring class
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.xml.internal.ws.client.EndpointIFInvocationHandler.invoke(Unknown Source)
at $Proxy17.getJobStatus(Unknown Source)
at compbio.ws.client.WSTester.testDefaultAlignment(Unknown Source)
at compbio.ws.client.WSTester.testMsaWS(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:684)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:486)
at jalview.gui.WsPreferences.editWsUrl_actionPerformed(WsPreferences.java:275)
at jalview.jbgui.GWsPreferences$16.mouseClicked(GWsPreferences.java:305)
at java.awt.AWTEventMulticaster.mouseClicked(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Componentjava.lang.ClassCastException: $Proxy17 cannot be cast to java.io.Closeable
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:684)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:486)
at jalview.gui.WsPreferences.editWsUrl_actionPerformed(WsPreferences.java:275)
at jalview.jbgui.GWsPreferences$16.mouseClicked(GWsPreferences.java:305)
at java.awt.AWTEventMulticaster.mouseClicked(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java..dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
<ServiceName> is not provided checking all known services...
Dec 17, 2012 3:54:02 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Checking service MafftWS
Testing alignment with default parameters:
Querying job status...FAILED
Exception while waiting for results. Exception details are below:
object is not an instance of declaring class
java.lang.IllegalArgumentException: object is not an instance of declaring class
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.xml.internal.ws.client.EndpointIFInvocationHandler.invoke(Unknown Source)
at $Proxy17.getJobStatus(Unknown Source)
at compbio.ws.client.WSTester.testDefaultAlignment(Unknown Source)
at compbio.ws.client.WSTester.testMsaWS(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:684)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:486)
at jalview.gui.WsPreferences.editWsUrl_actionPerformed(WsPreferences.java:275)
at jalview.jbgui.GWsPreferences$9.actionPerformed(GWsPreferences.java:224)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvjava.lang.ClassCastException: $Proxy17 cannot be cast to java.io.Closeable
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:684)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:486)
at jalview.gui.WsPreferences.editWsUrl_actionPerformed(WsPreferences.java:275)
at jalview.jbgui.GWsPreferences$9.actionPerformed(GWsPreferences.java:224)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
t.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)