Web Service Configuration Problem (JabAws)

Hello Jim,

my attempts at connecting to JABAWS from Jalview have failed.
It is a new install (never worked before) on a new computer where everything looked fine so far... but it must be a problem on my part since
http://www.compbio.dundee.ac.uk/jabaws/ServiceStatus reports that everything's running OK.

The error message in JalView is always the same, basically saying:
Web Service Configuration Problem: URLs not contacted: http://www.compbio.dundee.ac.uk/jabaws
go to Tools>Preferences in order to edit >Connections (but I don't use any proxy) or >Web services.

In the WebServices tab, I can't get
http://www.compbio.dundee.ac.uk/jabaws or
http://www.compbio.dundee.ac.uk:80/jabaws (as it appeared in the ServiceStatus report)
to be validated.

Please, find the log of the Java console as I failed editing the web service below (simply pressing OK after selecting jabaws for editing - no change).
I thank you in advance for giving it some of your time.

With my best regards,

Antoine

Jalview Desktop 2.8
Build Date: 12 November 2012
Java version: 1.6.0_01
x86 Windows Vista 6.1
<ServiceName> is not provided checking all known services...

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.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.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.run(Unknown Source)
java.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.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.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.run(Unknown Source)

Hi Antoine,

I'm guessing you've installed Jalview with the 'installAnywhere + Java' option. It turns out there's a known issue which we'll fix in the next release (see http://issues.jalview.org/browse/JAL-1220 ). The solution is to uninstall the version you have, install java from java.com, then install the 'No VM' Jalview install anywhere version.

If you have any more problems, it'd be helpful if you add a comment over at http://issues.jalview.org/browse/JAL-1220

Jim.

···

On 18/03/2013 10:50, Antoine Maillard wrote:

Hello Jim,

my attempts at connecting to JABAWS from Jalview have failed.
It is a new install (never worked before) on a new computer where
everything looked fine so far... but it must be a problem on my part since
http://www.compbio.dundee.ac.uk/jabaws/ServiceStatus reports that
everything's running OK.

The error message in JalView is always the same, basically saying:
Web Service Configuration Problem: URLs not contacted:
http://www.compbio.dundee.ac.uk/jabaws
go to Tools>Preferences in order to edit >Connections (but I don't
use any proxy) or >Web services.

In the WebServices tab, I can't get
http://www.compbio.dundee.ac.uk/jabaws or
http://www.compbio.dundee.ac.uk:80/jabaws (as it appeared in the
ServiceStatus report)
to be validated.

Please, find the log of the Java console as I failed editing the web
service below (simply pressing OK after selecting jabaws for editing -
no change).
I thank you in advance for giving it some of your time.

With my best regards,

Antoine

Jalview Desktop 2.8
Build Date: 12 November 2012
Java version: 1.6.0_01
x86 Windows Vista 6.1
<ServiceName> is not provided checking all known services...

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.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.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.run(Unknown Source)
java.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.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.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.run(Unknown Source)

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