[ome-users] OMERO Image archival (Leica)
josh.moore at gmx.de
josh.moore at gmx.de
Thu Jan 14 07:07:56 GMT 2010
Woodbridge, Mark R writes:
> Hi,
Hey Mark,
> I have uploaded a Leica SP2 dataset to OMERO by selecting the .lei
> file in Importer with archival enabled. The referenced image (.tif)
> files were uploaded automatically. Is it possible to download the
> original complete dataset (.lei + .tifs) using Insight? I can see
> options to download just the .lei file (which is automatically
> added as an attachment to each image) or to download individual
> images (which are composed of numerous tiff files) but can't see
> how to download the whole dataset.
There's currently no collapsing/merging of original files into a
single container (like a .tar or .zip). We've discussed various ways
of doing this (do it on import so there's only one attachment, etc.)
Feedback is very welcome.
> On a related issue, when I actually click the download arrow for an
> individual image Insight crashes with the attached stacktrace -
> does this happen for anyone else? Everything else seems to be
> working fine...
This is a known server-side problem:
https://trac.openmicroscopy.org.uk/omero/ticket/1614
which we thought we had worked around in the client. What version are
you using?
> Thanks for your help,
> Mark.
Gladly,
~Josh
> rg.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
> Cannot set the file's id.
> at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:449)
> at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:2744)
> at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.downloadFile(OmeroMetadataServiceImpl.java:1279)
> at org.openmicroscopy.shoola.env.data.views.calls.FilesLoader$1.doCall(FilesLoader.java:78)
> at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:145)
> at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
> at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
> at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
> at java.lang.Thread.run(Thread.java:619)
> Caused by: omero.InternalException
> serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (org.postgresql.util.PSQLException):
> Cannot change transaction read-only property in the middle of a transaction.
> at org.postgresql.jdbc2.AbstractJdbc2Connection.setReadOnly(AbstractJdbc2Connection.java:586)
> at bitronix.tm.resource.jdbc.lrc.LrcConnectionHandle.setReadOnly(LrcConnectionHandle.java:149)
> at bitronix.tm.resource.jdbc.JdbcConnectionHandle.setReadOnly(JdbcConnectionHandle.java:346)
> at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.getTargetConnection(LazyConnectionDataSourceProxy.java:398)
> at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:364)
> at $Proxy46.createStatement(Unknown Source)
> at sun.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at org.springframework.jdbc.datasource.TransactionAwareDataSourceProxy$TransactionAwareInvocationHandler.invoke(TransactionAwareDataSourceProxy.java:225)
> at $Proxy46.createStatement(Unknown Source)
> at sun.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedConnectionProxy.java:50)
> at $Proxy56.createStatement(Unknown Source)
> at ome.security.basic.EventHandler.invoke(EventHandler.java:110)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
> at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
> at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
> at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
> at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:175)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
> at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:100)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
> at $Proxy70.setFileId(Unknown Source)
> at sun.reflect.GeneratedMethodAccessor840.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:310)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
> at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:78)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
> at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:35)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
> at $Proxy70.setFileId(Unknown Source)
> at sun.reflect.GeneratedMethodAccessor889.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:616)
> at ome.services.blitz.util.IceMethodInvoker.callOrClose(IceMethodInvoker.java:257)
> at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
> at ome.services.throttling.Callback.run(Callback.java:55)
> at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:37)
> at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:115)
> at ome.services.blitz.impl.RawFileStoreI.setFileId_async(RawFileStoreI.java:55)
> at omero.api._RawFileStoreTie.setFileId_async(_RawFileStoreTie.java:78)
> at omero.api._RawFileStoreDisp.___setFileId(_RawFileStoreDisp.java:141)
> at omero.api._RawFileStoreDisp.__dispatch(_RawFileStoreDisp.java:284)
> at IceInternal.Incoming.invoke(Incoming.java:159)
> at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
> at Ice.ConnectionI.message(ConnectionI.java:972)
> at IceInternal.ThreadPool.run(ThreadPool.java:577)
> at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
> "
> serverExceptionClass = "ome.conditions.InternalException"
> message = " Wrapped Exception: (org.postgresql.util.PSQLException):
> Cannot change transaction read-only property in the middle of a transaction."
> 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:513)
> at java.lang.Class.newInstance0(Class.java:355)
> at java.lang.Class.newInstance(Class.java:308)
> at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
> at IceInternal.BasicStream.throwException(BasicStream.java:1632)
> at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
> at omero.api._RawFileStoreDelM.setFileId(_RawFileStoreDelM.java:138)
> at omero.api.RawFileStorePrxHelper.setFileId(RawFileStorePrxHelper.java:184)
> at omero.api.RawFileStorePrxHelper.setFileId(RawFileStorePrxHelper.java:156)
> at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:2742)
> ... 9 more
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
More information about the ome-users
mailing list