[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
Tue Aug 24 11:30:08 BST 2010
Hi Ron,
So it looks like you need to change the permissions of all the files
in /OMERO/ so that they are accessible by the user who is running the
current OMERO server (rtaylor)?
There are instructions for how to do this here:
http://www.openmicroscopy.org.uk/site/support/omero4/server/installation#section-4
Apparently the -R flag will mean that the change in owner is applied
recursively to everything in /OMERO/Pixels/ /OMERO/Thumbnails/ etc.
Hope this helps!
Will
On 24 Aug 2010, at 00:25, Taylor, Ronald C wrote:
>
> 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
>
>
>
>
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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