[ome-users] Problem with big images

[Josh Moore]

On Jun 14, 2012, at 5:17 PM, Josh Moore wrote:

> Hi Harri,
> 
> could you send the entire PixelData.log (off-list is fine)


Thanks for the files, Harri. Unfortunately, as you may have expected, there's nothing very helpful in there. A couple of options:

 * If you still have the initial log file from PixelData (the oldest of PixelData-9.log, etc) it *might* have more information about what's gone wrong.

 * If you don't have it but could restart the process, we'd be able to double-check that.

 * Failing that, we'll probably need to increase the log output to find out what's going wrong.

Just out of curiosity, what does "psql -h localhost -U omero omero -c 'select * from configuration' " say? (Replacing any values that are non-standard). Your main server shouldn't be functioning either if that table is missing, but perhaps there are no available DB connections to be had?

Cheers,
~Josh.


> ~J.
> 
> On Jun 14, 2012, at 4:54 PM, harri.jaalinoja at helsinki.fi wrote:
> 
>> 
>> Hello,
>> we have problems looking at big images. In the UI the image stays thumbnail sized, and in the logs I find these errors:
>> 
>> Blitz.log
>> 2012-06-14 17:31:18,548 INFO  [                ome.io.nio.PixelsService] (l.Server-1) Missing pyramid:/data/OMERO/Pixels/107_pyramid
>> 2012-06-14 17:31:18,549 INFO  [                 org.perf4j.TimingLogger] (l.Server-1) start[1339684278492] time[57] tag[omero.call.excepti
>> on]
>> 2012-06-14 17:31:18,549 INFO  [        ome.services.util.ServiceHandler] (l.Server-1)  Excp:    ome.conditions.MissingPyramidException: Mi
>> 
>> 
>> PixelData.log
>> 
>> 2012-06-14 17:44:52,019 ERROR [             org.quartz.core.JobRunShell] (3-thread-3) Job DEFAULT.pixelDataThreadRun threw an unhandled Exception:
>> org.springframework.scheduling.quartz.JobMethodInvocationFailedException: Invocation of method 'run' on target class [class ome.services.pixeldata.PixelDataThread] failed; nested exception is ome.conditions.InternalException: The configuration table seems to be missing
>> from your database. Please check your server installation instructions
>> for possible reasons.
>>      at org.springframework.scheduling.quartz.MethodInvokingJobDetailFactoryBean$MethodInvokingJob.executeInternal(MethodInvokingJobDetailFactoryBean.java:273)
>>      at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
>>      at org.quartz.core.JobRunShell.run(JobRunShell.java:203)
>>      at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
>>      at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
>>      at java.lang.Thread.run(Thread.java:722)
>> Caused by: ome.conditions.InternalException: The configuration table seems to be missing
>> from your database. Please check your server installation instructions
>> for possible reasons.
>>      at ome.services.eventlogs.PersistentEventLogLoader.getCurrentId(PersistentEventLogLoader.java:86)
>>      at ome.services.pixeldata.PersistentEventLogLoader.query(PersistentEventLogLoader.java:57)
>>      at ome.services.eventlogs.EventLogLoader.hasNext(EventLogLoader.java:137)
>>      at ome.services.pixeldata.PixelDataHandler.doWork(PixelDataHandler.java:81)
>> 
>> 
>> 
>> Indexer.log
>> 
>> 2012-06-14 17:35:12,026 ERROR [   ome.services.fulltext.FullTextIndexer] (3-thread-5) Unknown action type: PIXELDATA
>> 2012-06-14 17:35:32,025 ERROR [   ome.services.fulltext.FullTextIndexer] (3-thread-5) Unknown action type: PIXELDATA
>> 2012-06-14 17:35:40,034 ERROR [   ome.services.fulltext.FullTextIndexer] (3-thread-4) Unknown action type: PIXELDATA
>> 2012-06-14 17:35:44,039 ERROR [   ome.services.fulltext.FullTextIndexer] (3-thread-2) Unknown action type: PIXELDATA
>> 
>> 
>> 
>> What are we missing in the installation?
>> 
>> Thanks, best regards,
>> Harri
>> 
>> _______________________________________________
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>> ome-users at lists.openmicroscopy.org.uk
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> 
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