[ome-users] Query re the OMERO upgrade to OMERO 4.2.0 on a Mac server - images are completely dark
Will Moore
will at lifesci.dundee.ac.uk
Mon Aug 23 22:42:12 BST 2010
Hi Ron,
On 23 Aug 2010, at 22:30, Taylor, Ronald C wrote:
>
> Will,
>
> In case I wasn't clear in my earlier email, both the 4.1.1 and 4.2.0
> images should have been placed in the same directory. Omero.data.dir
> did not get changed, and we continued to use
> /OMERO/Pixels
>
> for storage.
>
> That is, the var omero.data.dir was set to "/OMERO/" in the ../
> omero_dist/etc/omero.properties file in both releases.
>
> So - the 4.1.1 image files appear to be missing, I think, and the
> omero.data.dir setting is not the cause.
The Pixels files are numbered by ID - generally this is the same as
the Image ID, which you can see in Insight.
So, you should be able to see whether all your 4.1 pixel data is in /
OMERO/Pixels/
I can't imagine how or why it would be deleted by the upgrade.
Will.
>
> Ron
>
>
> -----Original Message-----
> From: Taylor, Ronald C
> Sent: Monday, August 23, 2010 11:07 AM
> To: 'Will Moore'; ome-users at lists.openmicroscopy.org.uk; 'Josh Moore'
> Cc: ronald.taylor24 at gmail.com; Wiley, Steven; Taylor, Ronald C
> Subject: RE: [ome-users] Query re the OMERO upgrade to OMERO 4.2.0
> on a Mac server - images are completely dark
>
>
> Will,
>
> Re the permission issue: all the files in our
> /OMERO/Pixels
>
> directory have the same permission and the same owner (used 'ls -l'
> to look at them). So - that's not much help, I'm afraid.
>
> I also noticed that all ../Pixel and ../Thumbnail files have the
> same date - Aug 20th. I just went back to our Linux box and checked
> the files in /OMERO/Pixels there. Those files (carried over from
> 4.1.1) still have their June entry date.
>
> So - I'm thinking that the only files in ../Pixels on our Mac server
> are for the new images entered here since the 4.2.0 update (on Aug
> 20th), and that the files for the previous images got deleted
> somehow during the update process (unlike what happened on our Linux
> box, where the files remain). Hard to do a direct check as to what
> is there and what is not, since the files are labeled with numbers
> that only mean something to OMERO, but that's my thought.
>
> If you remember, I had a problem initially (a port problem with
> PostgreSQL) and "omero admin start" did not work the first time I
> invoked it on the Mac server. Could that aborted start, the first
> time 4.2.0 was invoked, have caused any such problem?
>
> What do you think?
> Ron
>
> ___________________________________________
> Ronald Taylor, Ph.D.
> Computational Biology & Bioinformatics Group Pacific Northwest
> National Laboratory
> 902 Battelle Boulevard
> P.O. Box 999, Mail Stop J4-33
> Richland, WA 99352 USA
> Office: 509-372-6568
> Email: ronald.taylor at pnl.gov
>
> -----Original Message-----
> From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
> Sent: Monday, August 23, 2010 6:13 AM
> To: Taylor, Ronald C
> Cc: ome-users at lists.openmicroscopy.org.uk; 'Josh Moore'; ronald.taylor24 at gmail.com
> ; Wiley, Steven
> Subject: Re: [ome-users] Query re the OMERO upgrade to OMERO 4.2.0
> on a Mac server - images are completely dark
>
> Hi Ron,
>
> The /OMERO/Pixels and /OMERO/Thumbnails will have corresponding
> entries for each image imported, but /OMERO/Files/ will not have
> corresponding entries.
> This is the repository for additional files, used to annotate
> Projects, Datasets, Images etc so it has nothing to do with your
> problem.
>
> I just tried to reproduce what you are seeing by deleting the /
> OMERO/ Pixels/ file for a particular image and then opening it in
> Insight.
> It seems that you don't get any errors (only a blank image with all
> the pixel values set to 0)!
> This is a bug - You should have got some error - I've made a ticket.
> http://trac.openmicroscopy.org.uk/shoola/ticket/1559
>
> But this doesn't explain why OMERO is not able to find the 4.1 pixel
> data.
>
> One possibility is permissions on the pixel files.
> Are there any differences in file permissions between the old 4.1
> files in /OMERO/Pixels and the new ones you've imported with 4.2?
>
> And are all the 4.2 pixel files being put in the same place as the
> 4.1 pixel files? (all in /OMRO/Pixels/ )?
>
> Any other differences you can find between 4.1 and 4.2 pixel data?
>
>
> Chris, Josh - Any possibility that some preferences or other
> configuration could be pointing to an invalid location for the 4.1
> pixel data?
>
> Cheers,
>
> Will.
>
>
> On 23 Aug 2010, at 03:36, Taylor, Ronald C wrote:
>
>>
>> Will,
>>
>> As my PNNL colleague Steve Wiley told me late on Friday (I see that
>> Steve Cced the omero list, so you should have seen his email), we can
>> enter new images into 4.2.0 on the Mac server and see them OK.
>> The image problem is confined to the images that got carried over
>> from
>> the 4.1.1 install. Those are the completely dark images.
>>
>> So - I'm thinking that the problem is not image display settings per
>> se, but rather that 4.2.0 cannot find the old images to display. As I
>> mentioned earlier, the previously entered images do get listed
>> properly on-screen - but they show up as just black boxes. There are
>> still entries for each old image in the db, but perhaps no path to
>> the
>> actual pixels?
>>
>> Question: I'm assuming that the actual pixel image gets stored in a
>> flat file in the directory
>> omero.data.dir/Pixels
>>
>> which would be this directory on our Mac server:
>>
>> /OMERO/Pixels
>>
>> I also noticed that there are many entries in ../Pixels (all the old
>> images?) which lack a corresponding file in /OMERO/Files
>>
>> That is, there is, for example, a file
>>
>> /OMERO/Pixels/101 (and a file /OMERO/Thumbnails/101)
>>
>> But no file
>>
>> /OMERO/Files/101
>>
>> Should not each ../Pixels file have a corresponding entry in ../
>> Files?
>>
>> Any thoughts on what to check in this regard?
>>
>> Ron
>>
>> ___________________________________________
>> Ronald Taylor, Ph.D.
>> Computational Biology & Bioinformatics Group Pacific Northwest
>> National Laboratory
>> 902 Battelle Boulevard
>> P.O. Box 999, Mail Stop J4-33
>> Richland, WA 99352 USA
>> Office: 509-372-6568
>> Email: ronald.taylor at pnl.gov
>>
>>
>> -----Original Message-----
>> From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
>> Sent: Saturday, August 21, 2010 3:31 AM
>> To: Taylor, Ronald C
>> Cc: 'Josh Moore'; ome-users at lists.openmicroscopy.org.uk;
>> ronald.taylor24 at gmail.com ; Wiley, Steven
>> Subject: Re: [ome-users] Query re the OMERO upgrade to OMERO 4.2.0 on
>> a Mac server - images are completely dark
>>
>> Hi Ron,
>>
>> I'm not sure what's going on - I would expect to see some error, but
>> you're not seeing anything like that?
>> Are you actually getting the pixel data (with messed-up rendering
>> settings) or is all the pixel data zeros?
>>
>> Try to use adjust the rendering settings, or use the measurement tool
>> to see if you actually have pixel values there E.g.
>> http://cvs.openmicroscopy.org.uk/snapshots/movies/omero-4-0/mov/
>> MeasurementTool-Taking%20Measurments.mov
>>
>> Will.
>>
>> On 20 Aug 2010, at 22:34, Taylor, Ronald C wrote:
>>
>>>
>>> Forgot to include diagnostics output - so, resending my help request
>>> with diags output at bottom.
>>> Ron
>>>
>>> -----Original Message-----
>>> From: Taylor, Ronald C
>>> Sent: Friday, August 20, 2010 2:22 PM
>>> To: 'Josh Moore'; ome-users at lists.openmicroscopy.org.uk
>>> Cc: ronald.taylor24 at gmail.com; Taylor, Ronald C; Wiley, Steven
>>> Subject: RE: [ome-users] need help with the OMERO upgrade to OMERO
>>> 4.2.0 on a Mac server - images are completely dark
>>>
>>>
>>> Hi Josh, everybody,
>>>
>>> Got 4.2.0 up and running on our Mac server, but initial testing
>>> shows
>>> that all our images come up completely dark. The images are still
>>> there - the file names get listed on-screen, but they appear on-
>>> screen as completely dark image boxes - no way to actually see them.
>>>
>>> So - this problem did not occur in the 4.2.0 upgrade on our Linux
>>> box.
>>> But the problem is definitely there on our Mac. Even when I do a
>>> "launch full viewer" the images come up black. Any ideas on what I
>>> should check?
>>>
>>> Does this perhaps have something to do with telling OMERO where its
>>> data directory is? I have checked the
>>> /Library/Omero/Versions/4.2.0/omero_dist/etc/omero_properties
>>>
>>> file, which shows
>>> omero.data.dir set to "/OMERO/"
>>>
>>> which appears to be correct - that was the previous setting for
>>> 4.1.1, and the subdirs in /OMERO/ show dates of "Aug20" (today), so
>>> Omero must have been accessing those directories today when I was
>>> testing the system. However, I see that all the thumbnail files have
>>> dates of today. Is that correct, or is something going wrong?
>>> The image files were previously in 4.1.1, so should not the
>>> thumbnails have been created long ago?
>>>
>>> Anyhoo - could use more guidance.
>>> Ron
>>>
>>> ___________________________________________
>>> Ronald Taylor, Ph.D.
>>> Computational Biology & Bioinformatics Group Pacific Northwest
>>> National Laboratory
>>> 902 Battelle Boulevard
>>> P.O. Box 999, Mail Stop J4-33
>>> Richland, WA 99352 USA
>>> Office: 509-372-6568
>>> Email: ronald.taylor at pnl.gov
>>>
>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>
>>>
>>> bash-3.2$ omero admin diagnostics
>>>
>>> =
>>> =
>>> ====================================================================
>>> ==========
>>> OMERO Diagnostics Beta-4.2.0-r7571-b29 =
>>> =
>>> ====================================================================
>>> ==========
>>>
>>> Commands: java -version 1.6.0 (/usr/bin/java
>>> -- 2 others)
>>> Commands: python -V 2.6.1 (/usr/bin/
>>> python)
>>> Commands: icegridnode --version 3.3.1 (/Library/Ice/
>>> Versions/3.3.1/bin/icegridnode)
>>> Commands: icegridadmin --version 3.3.1 (/Library/Ice/
>>> Versions/3.3.1/bin/icegridadmin)
>>> Commands: psql --version 8.3.11 (/Postgres/bin/
>>> psql)
>>>
>>> Server: icegridnode running
>>> Server: Blitz-0 active (pid = 21006,
>>> enabled)
>>> Server: DropBox active (pid = 21007,
>>> enabled)
>>> Server: FileServer active (pid = 21008,
>>> enabled)
>>> Server: Indexer-0 active (pid = 21009,
>>> enabled)
>>> Server: MonitorServer active (pid = 21010,
>>> enabled)
>>> Server: OMERO.Glacier2 active (pid = 21011,
>>> enabled)
>>> Server: OMERO.IceStorm active (pid = 21012,
>>> enabled)
>>> Server: Processor-0 active (pid = 21013,
>>> enabled)
>>> Server: Repository-1 error: node `repo'
>>> couldn't be reached:
>>> the node is not active
>>> Server: Tables-0 active (pid = 21014,
>>> enabled)
>>> Server: TestDropBox inactive (enabled)
>>>
>>> Log dir: /Library/Omero/Versions/4.2.0/omero_dist/var/log exists
>>>
>>> Log files: Blitz-0.log 1.0 MB
>>> errors=15 warnings=14
>>> Log files: DropBox.log 2.0 KB
>>> errors=1 warnings=3
>>> Log files: FileServer.log 0.0 KB
>>> Log files: Indexer-0.log 5.0 KB
>>> errors=0 warnings=9
>>> Log files: MonitorServer.log 2.0 KB
>>> errors=1 warnings=2
>>> Log files: OMEROweb.log 8.0 KB
>>> errors=22 warnings=0
>>> Log files: Processor-0.log 0.0 KB
>>> Log files: Tables-0.log 0.0 KB
>>> Log files: TestDropBox.log n/a
>>> Log files: master.err 0.0 KB
>>> Log files: master.out 0.0 KB
>>> Log files: Total size 1.22 MB
>>>
>>> Parsing Blitz-0.log:[line:17] => Server restarted <=
>>>
>>> Environment:OMERO_HOME=(unset)
>>>
>>> Environment:OMERO_NODE=(unset)
>>>
>>> Environment:OMERO_MASTER=(unset)
>>>
>>> Environment:PATH=/Library/Omero/Versions/4.2.0/omero_dist/bin:/usr/
>>> bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Postgres/bin:/
>>> Library/Java/Home/bin:/System/Library/Frameworks/JavaVM.framework/
>>> Versions/Current/Commands:/Library/Ice/Versions/3.3.1/bin
>>>
>>> Environment:ICE_HOME=/Library/Ice/Versions/3.3.1
>>>
>>> Environment:LD_LIBRARY_PATH=(unset)
>>>
>>> Environment:DYLD_LIBRARY_PATH=/Library/Frameworks/BerkeleyDB/
>>> Versions/4.6.21.NC/lib:/Library/Frameworks/expat/Versions/2.0.1/
>>> lib:/Library/PostgreSQL/Versions/8.3.11/lib:/Library/mcpp/Versions/
>>> 2.7.2/lib:/Library/Ice/Versions/3.3.1/lib:/Library/Frameworks/HDF5/
>>> Versions/1.8.4_patch1/lib
>>>
>>> bash-3.2$
>>> ----:**-F1 shell1 Bot
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
> William Moore
> Wellcome Trust Centre for Gene Regulation & Expression College of
> Life Sciences MSI/WTB/JBC Complex University of Dundee Dow Street
> Dundee DD1 5EH United Kingdom
>
> Phone 01382 386364
> http://openmicroscopy.org.uk
>
>
>
>
William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee DD1 5EH
United Kingdom
Phone 01382 386364
http://openmicroscopy.org.uk
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