[ome-users] VisBio errors
Curtis Rueden
ctrueden at wisc.edu
Mon Nov 26 17:59:22 GMT 2007
Hi Mario,
While there are a number of issues with the VisBio connectivity, your
Mac OS X exception is a bit surprising to me, and the Linux exception
looks like it might be a symptom of your hostname issues.
The Mac OS X exception indicates a problem loading an XML-RPC class,
which should be part of the VisBio WebStart distribution. So I'm not
sure what's going on there -- VisBio gives no such error on my Mac.
Instead, I get blank images, which I will be investigating in the next
few weeks as I spend some time working on the next (long overdue)
version of VisBio.
We also have plans to clean up the VisBio connectivity to allow use of
a local WebStart distribution (rather than the one on the LOCI site).
This should help some with stability issues -- a particular version of
OME server should come with a particular, known-to-work version of
VisBio.
-Curtis
On Nov 26, 2007 9:06 AM, Mario Valle <mvalle at cscs.ch> wrote:
> If you try to look at an image using VisBio, the following error appears on a Mac and no
> image is loaded. After this, I have another stack trace happening on Linux.
> Any clue?
> Thanks!
> mario
>
>
> java.lang.NoClassDefFoundError: org/apache/xmlrpc/XmlRpcClient
> at org.openmicroscopy.ds.DataServer.getDefaultCaller(DataServer.java:
> 90)
> at org.openmicroscopy.ds.DataServer.getDefaultServices
> (DataServer.java:113)
> at org.openmicroscopy.ds.DataServer.getDefaultServices
> (DataServer.java:103)
> at loci.visbio.ome.ImageDownloader.getSession(ImageDownloader.java:59)
> at loci.visbio.ome.OMEImage.initState(OMEImage.java:380)
> at loci.visbio.ome.OMEImage.<init>(OMEImage.java:136)
> at loci.visbio.ome.OMEImage.makeTransform(OMEImage.java:255)
> at loci.visbio.VisBioFrame.processArgument(VisBioFrame.java:308)
> at loci.visbio.VisBioFrame.processArguments(VisBioFrame.java:276)
> at loci.visbio.VisBioFrame.<init>(VisBioFrame.java:191)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance
> (NativeConstructorAccessorImpl.java:39)
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance
> (DelegatingConstructorAccessorImpl.java:27)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:274)
> at loci.visbio.VisBio.launch(VisBio.java:109)
> at loci.visbio.VisBio.main(VisBio.java:129)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke
> (NativeMethodAccessorImpl.java:39)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke
> (DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:324)
> at com.sun.javaws.Launcher.executeApplication(Launcher.java:1161)
> at com.sun.javaws.Launcher.executeMainClass(Launcher.java:1108)
> at com.sun.javaws.Launcher.continueLaunch(Launcher.java:951)
> at com.sun.javaws.Launcher.handleApplicationDesc(Launcher.java:522)
> at com.sun.javaws.Launcher.handleLaunchFile(Launcher.java:218)
> at com.sun.javaws.Launcher.run(Launcher.java:165)
> at java.lang.Thread.run(Thread.java:552)
>
>
> Stack trace on Linux
>
> org.openmicroscopy.ds.RemoteConnectionException
> at org.openmicroscopy.ds.XmlRpcCaller.invoke(XmlRpcCaller.java:233)
> at org.openmicroscopy.ds.XmlRpcCaller.dispatch(XmlRpcCaller.java:392)
> at org.openmicroscopy.ds.InstantiatingCaller.dispatchList(InstantiatingCaller.java:140)
> at org.openmicroscopy.ds.DataFactory.retrieveList(DataFactory.java:430)
> at loci.visbio.ome.ImageDownloader.retrieveImages(ImageDownloader.java:235)
> at loci.visbio.ome.ImageDownloader.downloadImage(ImageDownloader.java:94)
> at loci.visbio.ome.OMEImage.initState(OMEImage.java:384)
> at loci.visbio.ome.OMEImage.<init>(OMEImage.java:136)
> at loci.visbio.ome.OMEImage.makeTransform(OMEImage.java:255)
> at loci.visbio.VisBioFrame.processArgument(VisBioFrame.java:308)
> at loci.visbio.VisBioFrame.processArguments(VisBioFrame.java:276)
> at loci.visbio.VisBioFrame.<init>(VisBioFrame.java:191)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
> at java.lang.reflect.Constructor.newInstance(Unknown Source)
> at loci.visbio.VisBio.launch(VisBio.java:109)
> at loci.visbio.VisBio.main(VisBio.java:129)
> 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.javaws.Launcher.executeApplication(Unknown Source)
> at com.sun.javaws.Launcher.executeMainClass(Unknown Source)
> at com.sun.javaws.Launcher.continueLaunch(Unknown Source)
> at com.sun.javaws.Launcher.handleApplicationDesc(Unknown Source)
> at com.sun.javaws.Launcher.handleLaunchFile(Unknown Source)
> at com.sun.javaws.Launcher.run(Unknown Source)
> at java.lang.Thread.run(Unknown Source)
> Caused by: java.net.UnknownHostException: horus17
> at java.net.PlainSocketImpl.connect(Unknown Source)
> at java.net.SocksSocketImpl.connect(Unknown Source)
> at java.net.Socket.connect(Unknown Source)
> at java.net.Socket.connect(Unknown Source)
> at java.net.Socket.<init>(Unknown Source)
> at java.net.Socket.<init>(Unknown Source)
> at org.apache.xmlrpc.XmlRpcClientLite$HttpClient.initConnection(XmlRpcClientLite.java:339)
> at org.apache.xmlrpc.XmlRpcClientLite$HttpClient.<init>(XmlRpcClientLite.java:330)
> at org.apache.xmlrpc.XmlRpcClientLite$LiteWorker.execute(XmlRpcClientLite.java:193)
> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java:163)
> at org.openmicroscopy.ds.XmlRpcCaller.invoke(XmlRpcCaller.java:221)
> ... 28 more
> java.lang.NullPointerException
> at loci.visbio.ome.OMEImage.initState(OMEImage.java:386)
> at loci.visbio.ome.OMEImage.<init>(OMEImage.java:136)
> at loci.visbio.ome.OMEImage.makeTransform(OMEImage.java:255)
> at loci.visbio.VisBioFrame.processArgument(VisBioFrame.java:308)
> at loci.visbio.VisBioFrame.processArguments(VisBioFrame.java:276)
> at loci.visbio.VisBioFrame.<init>(VisBioFrame.java:191)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
> at java.lang.reflect.Constructor.newInstance(Unknown Source)
> at loci.visbio.VisBio.launch(VisBio.java:109)
> at loci.visbio.VisBio.main(VisBio.java:129)
> 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.javaws.Launcher.executeApplication(Unknown Source)
> at com.sun.javaws.Launcher.executeMainClass(Unknown Source)
> at com.sun.javaws.Launcher.continueLaunch(Unknown Source)
> at com.sun.javaws.Launcher.handleApplicationDesc(Unknown Source)
> at com.sun.javaws.Launcher.handleLaunchFile(Unknown Source)
> at com.sun.javaws.Launcher.run(Unknown Source)
> at java.lang.Thread.run(Unknown Source)
> org.openmicroscopy.ds.RemoteConnectionException
> at org.openmicroscopy.ds.XmlRpcCaller.invoke(XmlRpcCaller.java:233)
> at org.openmicroscopy.ds.XmlRpcCaller.login(XmlRpcCaller.java:291)
> at loci.visbio.ome.ImageDownloader.login(ImageDownloader.java:73)
> at loci.visbio.ome.OMEImage.initState(OMEImage.java:380)
> at loci.visbio.ome.OMEImage.<init>(OMEImage.java:152)
> at loci.visbio.ome.OMEImage.makeTransform(OMEImage.java:255)
> at loci.visbio.ome.OMEImage.makeTransform(OMEImage.java:202)
> 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 visad.util.ReflectedUniverse.exec(ReflectedUniverse.java:247)
> at loci.visbio.data.DataControls.actionPerformed(DataControls.java:516)
> 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.AbstractButton.doClick(Unknown Source)
> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
> at java.awt.Component.processMouseEvent(Unknown Source)
> at javax.swing.JComponent.processMouseEvent(Unknown Source)
> at java.awt.Component.processEvent(Unknown Source)
> at java.awt.Container.processEvent(Unknown Source)
> at java.awt.Component.dispatchEventImpl(Unknown Source)
> at java.awt.Container.dispatchEventImpl(Unknown Source)
> at java.awt.Component.dispatchEvent(Unknown Source)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
> at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
> at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
> at java.awt.Container.dispatchEventImpl(Unknown Source)
> at java.awt.Window.dispatchEventImpl(Unknown Source)
> at java.awt.Component.dispatchEvent(Unknown Source)
> at java.awt.EventQueue.dispatchEvent(Unknown Source)
> at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> at java.awt.EventDispatchThread.run(Unknown Source)
> Caused by: java.io.IOException: Unexpected Response from Server: Internal Server Error
> at org.apache.xmlrpc.XmlRpcClientLite$HttpClient.sendRequest(XmlRpcClientLite.java:402)
> at org.apache.xmlrpc.XmlRpcClientLite$LiteWorker.execute(XmlRpcClientLite.java:202)
> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java:163)
> at org.openmicroscopy.ds.XmlRpcCaller.invoke(XmlRpcCaller.java:221)
> ... 38 more
> java.lang.IllegalArgumentException: Have not logged in
> at org.openmicroscopy.ds.XmlRpcCaller.dispatch(XmlRpcCaller.java:383)
> at org.openmicroscopy.ds.InstantiatingCaller.dispatchList(InstantiatingCaller.java:140)
> at org.openmicroscopy.ds.DataFactory.retrieveList(DataFactory.java:430)
> at loci.visbio.ome.ImageDownloader.retrieveImages(ImageDownloader.java:235)
> at loci.visbio.ome.ImageDownloader.downloadImage(ImageDownloader.java:94)
> at loci.visbio.ome.OMEImage.initState(OMEImage.java:384)
> at loci.visbio.ome.OMEImage.<init>(OMEImage.java:152)
> at loci.visbio.ome.OMEImage.makeTransform(OMEImage.java:255)
> at loci.visbio.ome.OMEImage.makeTransform(OMEImage.java:202)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> at java.lang.reflect.Method.invoke(Unknown Source)
> at visad.util.ReflectedUniverse.exec(ReflectedUniverse.java:247)
> at loci.visbio.data.DataControls.actionPerformed(DataControls.java:516)
> at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
> at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
> at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
> at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
> at javax.swing.AbstractButton.doClick(Unknown Source)
> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
> at java.awt.Component.processMouseEvent(Unknown Source)
> at javax.swing.JComponent.processMouseEvent(Unknown Source)
> at java.awt.Component.processEvent(Unknown Source)
> at java.awt.Container.processEvent(Unknown Source)
> at java.awt.Component.dispatchEventImpl(Unknown Source)
> at java.awt.Container.dispatchEventImpl(Unknown Source)
> at java.awt.Component.dispatchEvent(Unknown Source)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
> at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
> at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
> at java.awt.Container.dispatchEventImpl(Unknown Source)
> at java.awt.Window.dispatchEventImpl(Unknown Source)
> at java.awt.Component.dispatchEvent(Unknown Source)
> at java.awt.EventQueue.dispatchEvent(Unknown Source)
> at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> at java.awt.EventDispatchThread.run(Unknown Source)
> java.lang.NullPointerException
> at loci.visbio.ome.OMEImage.initState(OMEImage.java:386)
> at loci.visbio.ome.OMEImage.<init>(OMEImage.java:152)
> at loci.visbio.ome.OMEImage.makeTransform(OMEImage.java:255)
> at loci.visbio.ome.OMEImage.makeTransform(OMEImage.java:202)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
> at java.lang.reflect.Method.invoke(Unknown Source)
> at visad.util.ReflectedUniverse.exec(ReflectedUniverse.java:247)
> at loci.visbio.data.DataControls.actionPerformed(DataControls.java:516)
> at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
> at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
> at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
> at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
> at javax.swing.AbstractButton.doClick(Unknown Source)
> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.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.pumpOneEventForHierarchy(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)
>
> --
> Ing. Mario Valle
> Visualization Group | http://www.cscs.ch/~mvalle
> Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60
> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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