[ome-devel] [OMERO] OMERO_Import 1.2 (linux) error
seb
Sebastien.Huart at curie.fr
Tue May 22 12:53:23 BST 2007
Hello,
I hope I'm not posting on the wrong list, sorry if I misunderstood the
purposes of this ML...
I had the following error, trying to upload files using the linux
version of OMERO_Import
(java version "1.6.0_01", debian linux 32 bit intel)
So I did the same with the MacOSX Import client, on the same server, to
make sure it was not a server-side problem and it worked as expected.
Here is the "Debug Output" from the importer.
I also copied and pasted below the console error messages.
Best regards,
sebastien
Debug Output
----------------------------------------------------------------
0 [Thread-3] (OMEROMetadataStore.java:130) DEBUG
ome.formats.OMEROMetadataStore - Initializing store: seb/<6chars>
ga-e0008o-6688.curie.fr:1099
13130 [Thread-4] (OMEROMetadataStore.java:369) DEBUG
ome.formats.OMEROMetadataStore - Setting Pixels: x (512), y (512), z
(19), c (3), t (1), PixelType (3), BigEndian? (false), dimemsionOrder
(XYZCT)
13279 [Thread-4] (OMEROMetadataStore.java:308) DEBUG
ome.formats.OMEROMetadataStore - Setting Dimensions: pixelSizeX
(0,132800), pixelSizeY (0,132800), pixelSizeZ (0,200000), pixelSizeC
(null), pixelSizeT (null)
13305 [Thread-4] (OMEROMetadataStore.java:253) DEBUG
ome.formats.OMEROMetadataStore - Setting Image: name
(/home/seb/data/Aude/RNAFISH_HbDig_WGA_DAPIjeune04_R3D.dv), creationDate
(null), description (null)
13324 [Thread-4] (OMEROMetadataStore.java:469) DEBUG
ome.formats.OMEROMetadataStore - Setting LogicalChannel: channelIdx
(0), name (null), ndFilter (0,501187), emWave (528), exWave (490),
photometicInterpretation (Monochrome), mode (Wide-field)
13524 [Thread-4] (OMEROMetadataStore.java:469) DEBUG
ome.formats.OMEROMetadataStore - Setting LogicalChannel: channelIdx
(1), name (null), ndFilter (1,000000), emWave (685), exWave (640),
photometicInterpretation (Monochrome), mode (Wide-field)
13703 [Thread-4] (OMEROMetadataStore.java:469) DEBUG
ome.formats.OMEROMetadataStore - Setting LogicalChannel: channelIdx
(2), name (null), ndFilter (0,100000), emWave (457), exWave (360),
photometicInterpretation (Monochrome), mode (Wide-field)
13875 [Thread-4] (OMEROMetadataStore.java:431) DEBUG
ome.formats.OMEROMetadataStore - Setting StageLabel: name (ome), x
(1889,373169), y (7785,993652), z (-21,978001)
13884 [Thread-4] (OMEROMetadataStore.java:516) DEBUG
ome.formats.OMEROMetadataStore - Setting GlobalMin: '387,000000'
GlobalMax: '3456,000000' for channel: '0'
13893 [Thread-4] (OMEROMetadataStore.java:516) DEBUG
ome.formats.OMEROMetadataStore - Setting GlobalMin: '1375,000000'
GlobalMax: '2570,000000' for channel: '1'
13895 [Thread-4] (OMEROMetadataStore.java:516) DEBUG
ome.formats.OMEROMetadataStore - Setting GlobalMin: '1252,000000'
GlobalMax: '3372,000000' for channel: '2'
13911 [Thread-4] (ImportLibrary.java:175) DEBUG
ome.formats.importer.ImportLibrary - Image Count: 57
15738 [Thread-4] (SocketClientInvoker.java:293) ERROR
org.jboss.remoting.transport.socket.SocketClientInvoker - Got
marshalling exception, exiting
15746 [Thread-4] (SocketClientInvoker.java:297) ERROR
org.jboss.remoting.transport.socket.SocketClientInvoker - Error loading
classes from remote call result.
------------------------------------------------------------------------
Console trace:
Exception in thread "Thread-4"
java.lang.reflect.UndeclaredThrowableException
at $Proxy9.setPixelsId(Unknown Source)
at
ome.formats.OMEROMetadataStore.setPlane(OMEROMetadataStore.java:579)
at
ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:266)
at
ome.formats.importer.ImportHandler.importImage(ImportHandler.java:229)
at
ome.formats.importer.ImportHandler.importImages(ImportHandler.java:147)
at
ome.formats.importer.ImportHandler.access$0(ImportHandler.java:89)
at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:80)
Caused by: javax.naming.NamingException: Could not dereference object
[Root exception is java.lang.reflect.UndeclaredThrowableException]
at
org.jnp.interfaces.NamingContext.getObjectInstanceWrapFailure(NamingContext.java:1150)
at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:705)
at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:587)
at javax.naming.InitialContext.lookup(InitialContext.java:392)
at
org.springframework.jndi.JndiTemplate$1.doInContext(JndiTemplate.java:124)
at
org.springframework.jndi.JndiTemplate.execute(JndiTemplate.java:86)
at
org.springframework.jndi.JndiTemplate.lookup(JndiTemplate.java:122)
at
org.springframework.jndi.JndiTemplate.lookup(JndiTemplate.java:147)
at
org.springframework.jndi.JndiLocatorSupport.lookup(JndiLocatorSupport.java:90)
at
org.springframework.jndi.JndiObjectLocator.lookup(JndiObjectLocator.java:101)
at
org.springframework.jndi.JndiObjectTargetSource.getTarget(JndiObjectTargetSource.java:121)
at
ome.client.JBossTargetSource.getTarget(JBossTargetSource.java:100)
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:184)
... 7 more
Caused by: java.lang.reflect.UndeclaredThrowableException
at $Proxy14.createProxy(Unknown Source)
at
org.jboss.ejb3.JndiProxyFactory.getObjectInstance(JndiProxyFactory.java:52)
at
javax.naming.spi.NamingManager.getObjectInstance(NamingManager.java:304)
at
org.jnp.interfaces.NamingContext.getObjectInstance(NamingContext.java:1125)
at
org.jnp.interfaces.NamingContext.getObjectInstanceWrapFailure(NamingContext.java:1142)
... 19 more
Caused by: java.lang.ClassNotFoundException:
[Lorg.jboss.aop.advice.Interceptor;
at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
at
org.jboss.remoting.loading.RemotingClassLoader.loadClass(RemotingClassLoader.java:50)
at
org.jboss.remoting.loading.ObjectInputStreamWithClassLoader.resolveClass(ObjectInputStreamWithClassLoader.java:139)
at
java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1575)
at
java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1496)
at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1624)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1323)
at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1945)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1869)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1753)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)
at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1945)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1869)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1753)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)
at
org.jboss.aop.joinpoint.InvocationResponse.readExternal(InvocationResponse.java:122)
at
java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1792)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1751)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)
at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1945)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1869)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1753)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)
at
org.jboss.remoting.serialization.impl.java.JavaSerializationManager.receiveObject(JavaSerializationManager.java:128)
at
org.jboss.remoting.marshal.serializable.SerializableUnMarshaller.read(SerializableUnMarshaller.java:66)
at
org.jboss.remoting.transport.socket.SocketClientInvoker.transport(SocketClientInvoker.java:279)
at
org.jboss.remoting.RemoteClientInvoker.invoke(RemoteClientInvoker.java:143)
at org.jboss.remoting.Client.invoke(Client.java:525)
at org.jboss.remoting.Client.invoke(Client.java:488)
at
org.jboss.aspects.remoting.InvokeRemoteInterceptor.invoke(InvokeRemoteInterceptor.java:55)
at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)
at
org.jboss.aspects.remoting.IsLocalInterceptor.invoke(IsLocalInterceptor.java:48)
at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:101)
at org.jboss.aspects.remoting.PojiProxy.invoke(PojiProxy.java:61)
... 24 more
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