[ome-users] Importer failed: wrong pathname generated?

Mon Jul 7 14:00:28 BST 2008

Dear list members,

We have just installed Omero 3.0.1beta and everything seems to be working
except when we try to import an image.

After clicking 'Import', the status is 'failed' - the debug messages are
attached below.

The directory on the omero server is /data/omero, but it seems like the
wrong path is generated (1st line of debug messages) as /data/omeroPixels/64
is requested (which doesn't exist of course) - maybe a missing slash?

Many thanks,

Guenter.

ome.conditions.ResourceError: /data/omeroPixels/64 (No such file or
directory)
	at
ome.services.RawPixelsBean.handleException(RawPixelsBean.java:521)
	at ome.services.RawPixelsBean.setPlane(RawPixelsBean.java:440)
	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:597)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:11
2)
	at
org.jboss.ejb3.interceptor.InvocationContextImpl.proceed(InvocationContextIm
pl.java:166)
	at ome.tools.spring.AOPAdapter.invokeJoinpoint(AOPAdapter.java:53)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:149)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:112)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:171)
	at
ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:173)
	at
ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:158)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:171)
	at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(Tr
ansactionInterceptor.java:106)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:171)
	at
ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter
.java:169)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:171)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:93)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:171)
	at
org.springframework.aop.interceptor.AbstractTraceInterceptor.invoke(Abstract
TraceInterceptor.java:113)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:171)
	at
ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:79)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:171)
	at
ome.services.util.OmeroAroundInvoke.call(OmeroAroundInvoke.java:161)
	at
ome.services.util.OmeroAroundInvoke.loginAndSpringWrap(OmeroAroundInvoke.jav
a:134)
	at sun.reflect.GeneratedMethodAccessor349.invoke(Unknown Source)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl
.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at
org.jboss.ejb3.interceptor.InvocationContextImpl.proceed(InvocationContextIm
pl.java:118)
	at
org.jboss.ejb3.interceptor.EJB3InterceptorsInterceptor.invoke(EJB3Intercepto
rsInterceptor.java:63)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.entity.ExtendedPersistenceContextPropagationInterceptor.invok
e(ExtendedPersistenceContextPropagationInterceptor.java:57)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.entity.TransactionScopedEntityManagerInterceptor.invoke(Trans
actionScopedEntityManagerInterceptor.java:54)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.AllowedOperationsInterceptor.invoke(AllowedOperationsIntercep
tor.java:47)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.tx.BMTInterceptor.handleStateful(BMTInterceptor.java:106)
	at org.jboss.ejb3.tx.BMTInterceptor.invoke(BMTInterceptor.java:132)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.aspects.tx.TxPropagationInterceptor.invoke(TxPropagationIntercepto
r.java:76)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.stateful.StatefulInstanceInterceptor.invoke(StatefulInstanceI
nterceptor.java:83)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.aspects.security.AuthenticationInterceptor.invoke(AuthenticationIn
terceptor.java:77)
	at
org.jboss.ejb3.security.Ejb3AuthenticationInterceptor.invoke(Ejb3Authenticat
ionInterceptor.java:106)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.ENCPropagationInterceptor.invoke(ENCPropagationInterceptor.ja
va:46)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.asynchronous.AsynchronousInterceptor.invoke(AsynchronousInter
ceptor.java:106)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.stateful.StatefulContainer.dynamicInvoke(StatefulContainer.ja
va:333)
	at org.jboss.aop.Dispatcher.invoke(Dispatcher.java:106)
	at
org.jboss.aspects.remoting.AOPRemotingInvocationHandler.invoke(AOPRemotingIn
vocationHandler.java:82)
	at org.jboss.remoting.ServerInvoker.invoke(ServerInvoker.java:734)
	at
org.jboss.remoting.transport.socket.ServerThread.processInvocation(ServerThr
ead.java:560)
	at
org.jboss.remoting.transport.socket.ServerThread.dorun(ServerThread.java:369
)
	at
org.jboss.remoting.transport.socket.ServerThread.run(ServerThread.java:165)
	at
org.jboss.remoting.MicroRemoteClientInvoker.invoke(MicroRemoteClientInvoker.
java:163)
	at org.jboss.remoting.Client.invoke(Client.java:1550)
	at org.jboss.remoting.Client.invoke(Client.java:530)
	at
org.jboss.aspects.remoting.InvokeRemoteInterceptor.invoke(InvokeRemoteInterc
eptor.java:62)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.aspects.tx.ClientTxPropagationInterceptor.invoke(ClientTxPropagati
onInterceptor.java:61)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.aspects.security.SecurityClientInterceptor.invoke(SecurityClientIn
terceptor.java:53)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.remoting.IsLocalInterceptor.invoke(IsLocalInterceptor.java:72
)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.stateful.StatefulRemoteProxy.invoke(StatefulRemoteProxy.java:
135)
	at $Proxy18.setPlane(Unknown Source)
	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
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopU
tils.java:296)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint
(ReflectiveMethodInvocation.java:177)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:144)
	at ome.client.Interceptor.invoke(Interceptor.java:47)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:166)
	at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopPro
xy.java:204)
	at $Proxy16.setPlane(Unknown Source)
	at
ome.formats.OMEROMetadataStore.setPlane(OMEROMetadataStore.java:398)
	at
ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:467)
	at
ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:395)
	at
ome.formats.importer.ImportHandler.importImages(ImportHandler.java:172)
	at
ome.formats.importer.ImportHandler.access$0(ImportHandler.java:106)
	at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:87)
	at
org.jboss.aspects.remoting.InvokeRemoteInterceptor.invoke(InvokeRemoteInterc
eptor.java:74)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.aspects.tx.ClientTxPropagationInterceptor.invoke(ClientTxPropagati
onInterceptor.java:61)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.aspects.security.SecurityClientInterceptor.invoke(SecurityClientIn
terceptor.java:53)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.remoting.IsLocalInterceptor.invoke(IsLocalInterceptor.java:72
)
	at
org.jboss.aop.joinpoint.MethodInvocation.invokeNext(MethodInvocation.java:10
1)
	at
org.jboss.ejb3.stateful.StatefulRemoteProxy.invoke(StatefulRemoteProxy.java:
135)
	at $Proxy18.setPlane(Unknown Source)
	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
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopU
tils.java:296)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint
(ReflectiveMethodInvocation.java:177)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:144)
	at ome.client.Interceptor.invoke(Interceptor.java:47)
	at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(Reflect
iveMethodInvocation.java:166)
	at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopPro
xy.java:204)
	at $Proxy16.setPlane(Unknown Source)
	at
ome.formats.OMEROMetadataStore.setPlane(OMEROMetadataStore.java:398)
	at
ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:467)
	at
ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:395)
	at
ome.formats.importer.ImportHandler.importImages(ImportHandler.java:172)
	at
ome.formats.importer.ImportHandler.access$0(ImportHandler.java:106)
	at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:87)

------------------------------------------
Dr. Guenter Giese
Light Microscopy Facility Manager
Dept. of Biomedical Optics
MPI fuer Medizinische Forschung Jahnstr. 29
D-69120 Heidelberg, Germany
Phone (+49) 6221-486-360 (Fax: -325)
e-mail: guenter.giese at mpimf-heidelberg.mpg.de 