[ome-users] Importing LEICA .lif files into OMERO beta4
Caterina Strambio De Castillia
strambc at mail.rockefeller.edu
Thu Apr 2 15:06:47 BST 2009
Dear OMERO community,
I have had problems importing Leica .lif files into the OMERO beta4
DB using the latest release of the OMERO.importer.
The error message I got is reported at the bottom of the message.
Please advise
Best
Caterina
____________
java.lang.RuntimeException: omero.InternalException
serverStackTrace = "ome.conditions.InternalException: Wrapped
Exception: (java.lang.IndexOutOfBoundsException):
Index: 3, Size: 3
at java.util.ArrayList.RangeCheck
(ArrayList.java:546)
at java.util.ArrayList.get(ArrayList.java:321)
at ome.model.core.Pixels.getChannel
(Pixels.java:1261)
at ome.formats.OMEROMetadataStore.getChannel
(OMEROMetadataStore.java:717)
at ome.formats.OMEROMetadataStore.handle
(OMEROMetadataStore.java:359)
at
ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:138)
at ome.services.blitz.impl.MetadataStoreI
$4.doWork(MetadataStoreI.java:144)
at
sun.reflect.GeneratedMethodAccessor526.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke
(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke
(Method.java:585)
at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(
AopUtils.java:310)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinp
oint(ReflectiveMethodInvocation.java:182)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:149)
at ome.services.util.Executor$Impl
$Interceptor.invoke(Executor.java:377)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at ome.security.basic.EventHandler.invoke
(EventHandler.java:116)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at
org.springframework.orm.hibernate3.HibernateInterceptor.invoke
(HibernateInterceptor.java:111)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invok
e(TransactionInterceptor.java:106)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at ome.tools.hibernate.ProxyCleanupFilter
$Interceptor.invoke(ProxyCleanupFilter.java:169)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at ome.services.util.ServiceHandler.invoke
(ServiceHandler.java:97)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke
(JdkDynamicAopProxy.java:204)
at $Proxy55.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute
(Executor.java:307)
at ome.services.throttling.Adapter.run
(Adapter.java:50)
at
ome.services.throttling.InThreadThrottlingStrategy.runnableCall
(InThreadThrottlingStrategy.java:51)
at
ome.services.blitz.impl.AbstractAmdServant.runnableCall
(AbstractAmdServant.java:128)
at
ome.services.blitz.impl.MetadataStoreI.updateObjects_async
(MetadataStoreI.java:129)
at
omero.api._MetadataStoreTie.updateObjects_async
(_MetadataStoreTie.java:85)
at
omero.api._MetadataStoreDisp.___updateObjects(_MetadataStoreDisp.java:
166)
at omero.api._MetadataStoreDisp.__dispatch
(_MetadataStoreDisp.java:308)
at IceInternal.Incoming.invoke
(Incoming.java:166)
at Ice.ConnectionI.invokeAll
(ConnectionI.java:2045)
at Ice.ConnectionI.message(ConnectionI.java:
977)
at IceInternal.ThreadPool.run
(ThreadPool.java:575)
at IceInternal.ThreadPool.access$100
(ThreadPool.java:12)
at IceInternal.ThreadPool
$EventHandlerThread.run(ThreadPool.java:951)
"
serverExceptionClass = "ome.conditions.InternalException"
message = " Wrapped Exception:
(java.lang.IndexOutOfBoundsException):
Index: 3, Size: 3"
at ome.formats.OMEROMetadataStoreClient.saveToDB
(OMEROMetadataStoreClient.java:2247)
at ome.formats.importer.ImportLibrary.importMetadata
(ImportLibrary.java:239)
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:
328)
at ome.formats.importer.ImportHandler.importImages
(ImportHandler.java:181)
at ome.formats.importer.ImportHandler.access$0(ImportHandler.java:107)
at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:88)
Caused by: omero.InternalException
serverStackTrace = "ome.conditions.InternalException: Wrapped
Exception: (java.lang.IndexOutOfBoundsException):
Index: 3, Size: 3
at java.util.ArrayList.RangeCheck
(ArrayList.java:546)
at java.util.ArrayList.get(ArrayList.java:321)
at ome.model.core.Pixels.getChannel
(Pixels.java:1261)
at ome.formats.OMEROMetadataStore.getChannel
(OMEROMetadataStore.java:717)
at ome.formats.OMEROMetadataStore.handle
(OMEROMetadataStore.java:359)
at
ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:138)
at ome.services.blitz.impl.MetadataStoreI
$4.doWork(MetadataStoreI.java:144)
at
sun.reflect.GeneratedMethodAccessor526.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke
(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke
(Method.java:585)
at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(
AopUtils.java:310)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinp
oint(ReflectiveMethodInvocation.java:182)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:149)
at ome.services.util.Executor$Impl
$Interceptor.invoke(Executor.java:377)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at ome.security.basic.EventHandler.invoke
(EventHandler.java:116)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at
org.springframework.orm.hibernate3.HibernateInterceptor.invoke
(HibernateInterceptor.java:111)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invok
e(TransactionInterceptor.java:106)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at ome.tools.hibernate.ProxyCleanupFilter
$Interceptor.invoke(ProxyCleanupFilter.java:169)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at ome.services.util.ServiceHandler.invoke
(ServiceHandler.java:97)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
(ReflectiveMethodInvocation.java:171)
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke
(JdkDynamicAopProxy.java:204)
at $Proxy55.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute
(Executor.java:307)
at ome.services.throttling.Adapter.run
(Adapter.java:50)
at
ome.services.throttling.InThreadThrottlingStrategy.runnableCall
(InThreadThrottlingStrategy.java:51)
at
ome.services.blitz.impl.AbstractAmdServant.runnableCall
(AbstractAmdServant.java:128)
at
ome.services.blitz.impl.MetadataStoreI.updateObjects_async
(MetadataStoreI.java:129)
at
omero.api._MetadataStoreTie.updateObjects_async
(_MetadataStoreTie.java:85)
at
omero.api._MetadataStoreDisp.___updateObjects(_MetadataStoreDisp.java:
166)
at omero.api._MetadataStoreDisp.__dispatch
(_MetadataStoreDisp.java:308)
at IceInternal.Incoming.invoke
(Incoming.java:166)
at Ice.ConnectionI.invokeAll
(ConnectionI.java:2045)
at Ice.ConnectionI.message(ConnectionI.java:
977)
at IceInternal.ThreadPool.run
(ThreadPool.java:575)
at IceInternal.ThreadPool.access$100
(ThreadPool.java:12)
at IceInternal.ThreadPool
$EventHandlerThread.run(ThreadPool.java:951)
"
serverExceptionClass = "ome.conditions.InternalException"
message = " Wrapped Exception:
(java.lang.IndexOutOfBoundsException):
Index: 3, Size: 3"
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance
(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance
(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:494)
at java.lang.Class.newInstance0(Class.java:350)
at java.lang.Class.newInstance(Class.java:303)
at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow
(BasicStream.java:2127)
at IceInternal.BasicStream.throwException(BasicStream.java:1541)
at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
at omero.api._MetadataStoreDelM.updateObjects
(_MetadataStoreDelM.java:177)
at omero.api.MetadataStorePrxHelper.updateObjects
(MetadataStorePrxHelper.java:254)
at omero.api.MetadataStorePrxHelper.updateObjects
(MetadataStorePrxHelper.java:226)
at ome.formats.OMEROMetadataStoreClient.saveToDB
(OMEROMetadataStoreClient.java:2230)
... 5 more
____________________________
Caterina Strambio De Castillia, Dottore in Biologia, PhD
Biologiste 2 - Senior Research Scientist
Laboratory of Viral replication, pathogenesis, and immunity
http://www.mimo.unige.ch/luban_lab/
Department of Microbiology and Molecular Medicine
University of Geneva
1 Rue Michel Servet
CH-1211 Geneva 4
Switzerland
Phone: +41-22-379-5720
Fax: +41-22-379-5702
****
Visiting Fellow
Laboratory of Cellular and Structural Biology
http://www.rockefeller.edu/labheads/rout/research_project_3.php
The Rockefeller University
1230 York Avenue
New York NY 10065
______________________________
Caterina Strambio De Castillia
via Monte Crenone 1
6500 Bellinzona
Svizzera
+41 91 8252701
+41 78 7367537
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