[ome-users] Channel issue with single tif files and OMERO.server
Simon Li
s.p.li at dundee.ac.uk
Thu Apr 24 15:34:44 BST 2014
Hi Jan
Thanks for uploading the server log files. OMERO should handle UTF-8 correctly, it looks like one of the file names has become corrupted somewhere along the line. Are you able to test the import on other platforms, for instance from a Mac?
Could you send us the insight log file from one of your affected users? You should be able to obtain the log file in Insight by going to the Help menu, Show log file.
Thanks
Simon
On 24 Apr 2014, at 10:34, Jan Eglinger <jan.eglinger at gmail.com>
wrote:
> Hi Simon,
>
> thanks for your reply. I've pasted the output of diagnostics and config below. In the meantime, some more files became faulty, and I noticed that these were all files that contain an Umlaut (e.g. ä or ü). Looking at the errors in Blitz-0.log, I also noticed that those non-ASCII characters were apparently replaced by question marks in some requests.
> I will upload the log files in a minute.
>
> Not sure if it's relevant, but the files containing non-ASCII characters were uploaded with client (on WinXP) and server running on version 5.0.0 and it was only after seeing this issue that I updated the server to 5.0.1 to see if the issue persists.
>
> As a work-around, I have advised the concerned users to avoid non-ASCII characters in their files, but of course it would be nice having full UTF-8 compatibility.
>
> Cheers,
> Jan
>
> > Output of `omero admin diagnostics`
>
> ================================================================================
> OMERO Diagnostics 5.0.1-ice35-b21
> ================================================================================
>
> Commands: java -version 1.7.0 (/usr/bin/java)
> Commands: python -V 2.6.6 (/usr/bin/python)
> Commands: icegridnode --version 3.5.1 (/usr/bin/icegridnode)
> Commands: icegridadmin --version 3.5.1 (/usr/bin/icegridadmin)
> Commands: psql --version 8.4.20 (/usr/bin/psql)
>
> Server: icegridnode running
> Server: Blitz-0 active (pid = 13032, enabled)
> Server: DropBox active (pid = 13046, enabled)
> Server: FileServer active (pid = 13054, enabled)
> Server: Indexer-0 active (pid = 13055, enabled)
> Server: MonitorServer active (pid = 13056, enabled)
> Server: OMERO.Glacier2 active (pid = 13058, enabled)
> Server: OMERO.IceStorm active (pid = 13063, enabled)
> Server: PixelData-0 active (pid = 13060, enabled)
> Server: Processor-0 active (pid = 13079, enabled)
> Server: Tables-0 inactive (disabled)
> Server: TestDropBox inactive (enabled)
>
> OMERO: SSL port 4064
> OMERO: TCP port 4063
>
> Log dir: /home/eglinger-omero/apps/OMERO/OMERO.server/var/log exists
>
> Log files: Blitz-0.log 3.0 MB errors=37 warnings=13
> Log files: DropBox.log 1.0 KB
> Log files: FileServer.log 0.0 KB
> Log files: Indexer-0.log 20.0 KB errors=1 warnings=2
> Log files: MonitorServer.log 1.0 KB
> Log files: OMEROweb.log 1.0 MB errors=90 warnings=0
> Log files: OMEROweb_request.log 0.0 KB
> Log files: PixelData-0.log 21.0 KB errors=1 warnings=2
> Log files: Processor-0.log 0.0 KB
> Log files: Tables-0.log n/a
> Log files: TestDropBox.log n/a
> Log files: master.err 0.0 KB errors=1 warnings=0
> Log files: master.out 0.0 KB
> Log files: Total size 5.38 MB
>
>
> Environment:OMERO_HOME=(unset)
> Environment:OMERO_NODE=(unset)
> Environment:OMERO_MASTER=(unset)
> Environment:OMERO_TEMPDIR=(unset)
> Environment:PATH=/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/bin:/usr/share/Ice-3.5.1:/usr/bin:/home/eglinger-omero/apps/OMERO/OMERO.server/bin:/home/eglinger-omero/bin
> Environment:ICE_HOME=/usr/share/Ice-3.5.1
> Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
> Environment:DYLD_LIBRARY_PATH=(unset)
>
> OMERO data dir: '/home/eglinger-omero/apps/OMERO/OMERO.data'Exists? TrueIs writable? True
> OMERO temp dir: '/home/eglinger-omero/omero/tmp'Exists? TrueIs writable? True (Size: 0)
> OMERO.web status... [RUNNING] (PID 13279)
>
>
> > Output of `omero config get`
>
> omero.data.dir=/home/eglinger-omero/apps/OMERO/OMERO.data
> omero.db.name=omedb
> omero.db.pass=*******
> omero.db.user=*******
> omero.web.application_server=fastcgi-tcp
> omero.web.debug=True
>
>
>
> On 23.04.2014, 11:03 AM, Simon Li wrote:
>> Hi Jan
>>
>> Could you send us the following information please:
>>
>> Output of `omero admin diagnostics`
>> Output of `omero config get` (Blank out any usernames/passwords)
>> Your server logs- zip them up and upload them to https://www.openmicroscopy.org/qa2/qa/upload/
>> If your server has been running for a while you can just send us the most recent log-files.
>>
>> Many thanks
>>
>> Simon
>>
>>
>> On 22 Apr 2014, at 14:11, Jan Eglinger <jan.eglinger at gmail.com> wrote:
>>
>>> Dear ome developers and users,
>>>
>>> I'm having a problem with single channel tif images uploaded to OMERO.server: while most of them are displayed and downloaded correctly, some of them (only after a while) cannot be displayed nor downloaded any more, while their thumbnails are still displayed.
>>>
>>> In the "General" information tab on OMERO.web, it says: "Channels: No channel specified". The full viewer displays "Error instantiating pixel buffer".
>>> When I run the 'Combine Images...' script, I get the traceback pasted below.
>>>
>>> What puzzles me is that the very same images have been accessible already, only now they have become inaccessible. Uploading the same files again (in a different dataset) works as expected.
>>>
>>> Any idea what might be wrong?
>>>
>>> Thanks,
>>> Jan
>>>
>>>
>>>
>>> Traceback (most recent call last):
>>> File "./script", line 655, in <module>
>>> runAsScript()
>>> File "./script", line 641, in runAsScript
>>> images, message = combineImages(conn, parameterMap)
>>> File "./script", line 483, in combineImages
>>> dataset, colourMap)
>>> File "./script", line 384, in makeSingleImage
>>> plane2D = getPlane(rawPixelStore, pixels, planeZ, 0, 0)
>>> File "./script", line 101, in getPlane
>>> rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
>>> File "/home/eglinger-omero/apps/OMERO/OMERO.server/lib/python/omero_api_RawPixelsStore_ice.py", line 422, in setPixelsId
>>> return _M_omero.api.RawPixelsStore._op_setPixelsId.invoke(self, ((pixelsId, bypassOriginalFile), _ctx))
>>> omero.ResourceError: exception ::omero::ResourceError
>>> {
>>> serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /home/eglinger-omero/apps/OMERO/OMERO.data/ManagedRepository/group03_7/2014-04/10/17-19-33.573/2Mutant Insulin und Glucagon (grün) 20x.tif
>>> at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:787)
>>> at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:550)
>>> at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:468)
>>> at ome.services.RawPixelsBean.setPixelsId(RawPixelsBean.java:272)
>>> at sun.reflect.GeneratedMethodAccessor626.invoke(Unknown Source)
>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>> at java.lang.reflect.Method.invoke(Method.java:606)
>>> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
>>> at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>> at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:218)
>>> at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:202)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>> at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>> at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>> at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
>>> at com.sun.proxy.$Proxy89.setPixelsId(Unknown Source)
>>> at sun.reflect.GeneratedMethodAccessor626.invoke(Unknown Source)
>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>> at java.lang.reflect.Method.invoke(Method.java:606)
>>> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
>>> at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>> at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
>>> at com.sun.proxy.$Proxy89.setPixelsId(Unknown Source)
>>> at sun.reflect.GeneratedMethodAccessor742.invoke(Unknown Source)
>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>> at java.lang.reflect.Method.invoke(Method.java:606)
>>> at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
>>> at ome.services.throttling.Callback.run(Callback.java:56)
>>> at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
>>> at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149)
>>> at ome.services.blitz.impl.RawPixelsStoreI.setPixelsId_async(RawPixelsStoreI.java:194)
>>> at sun.reflect.GeneratedMethodAccessor741.invoke(Unknown Source)
>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>> at java.lang.reflect.Method.invoke(Method.java:606)
>>> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
>>> at omero.cmd.CallContext.invoke(CallContext.java:78)
>>> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>>> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
>>> at com.sun.proxy.$Proxy90.setPixelsId_async(Unknown Source)
>>> at omero.api._RawPixelsStoreTie.setPixelsId_async(_RawPixelsStoreTie.java:258)
>>> at omero.api._RawPixelsStoreDisp.___setPixelsId(_RawPixelsStoreDisp.java:634)
>>> at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1530)
>>> at IceInternal.Incoming.invoke(Incoming.java:222)
>>> at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
>>> at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
>>> at Ice.ConnectionI.message(ConnectionI.java:1213)
>>> at IceInternal.ThreadPool.run(ThreadPool.java:321)
>>> at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
>>> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
>>> at java.lang.Thread.run(Thread.java:744)
>>>
>>> serverExceptionClass = ome.conditions.ResourceError
>>> message = Error instantiating pixel buffer: /home/eglinger-omero/apps/OMERO/OMERO.data/ManagedRepository/group03_7/2014-04/10/17-19-33.573/2Mutant Insulin und Glucagon (grün) 20x.tif
>>> }
>
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