[ome-users] Channel issue with single tif files and OMERO.server
Jan Eglinger
jan.eglinger at gmail.com
Thu Apr 24 10:34:08 BST 2014
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?
True Is writable? True
OMERO temp dir: '/home/eglinger-omero/omero/tmp' Exists? True Is
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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