[ome-users] Query re the OMERO upgrade to OMERO 4.2.0 on a Mac server - images are completely dark
Taylor, Ronald C
ronald.taylor at pnl.gov
Tue Aug 24 00:25:06 BST 2010
The mystery deepens. There are indeed entries for the old images in ../Pixels and ../Images. The images did not get deleted during the upgrade to 4.2.0. (I matched on Image ID --> filename).
But - the old images still are completely black. Brought a couple up again (double-clicking on the thumbnail) in the separate viewer window and twiddled parameters, but the images remain fully black. Newly loaded images from after the upgrade look fine, as I said earlier. Both old and new images are in the same 'default' group.
We did not have a huge number of old images, so we can reenter them. But I would like to find out what is going on.
So - any ideas?
Ron
-----Original Message-----
From: Taylor, Ronald C
Sent: Monday, August 23, 2010 3:23 PM
To: 'Will Moore'
Cc: 'Josh Moore'; Taylor, Ronald C; ronald.taylor24 at gmail.com
Subject: RE: [ome-users] Query re the OMERO upgrade to OMERO 4.2.0 on a Mac server - images are completely dark
Will,
The only thing difference that I can think of is that the missing images were uploaded by my colleague Steve Wiley into his own OMERO account while he ran the OMERO importer client in his own OS X account on the Mac server, while PostgreSQL and the Omero system was running in the different "rontaylor" OS X acct. And I was running in the "rontaylor" account during the upgrade on the Mac server.
On the Linux box, where there was not any problem, the images were uploaded by me operating as the Linux "rtaylor" user (uploaded into the OMERO "root" account), with OMERO also running in the same Linux "rtaylor" account. So - maybe something to do with file permissions? Still don't know why that would cause files to get erased, though.
I'll confirm that the only image files now present in /OMERO/Pixels are new ones by checking the Image ID numbers, as you suggest. Just have to wait for Steve read his email and give me his Omero acct password to get access to his images. I'll get back to you if I find any old files at all still present.
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 2:42 PM
To: Taylor, Ronald C
Cc: ome-users at lists.openmicroscopy.org.uk; 'Josh Moore'; ronald.taylor24 at gmail.com
Subject: Re: [ome-users] Query re the OMERO upgrade to OMERO 4.2.0 on a Mac server - images are completely dark
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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