Open Microscopy Environment

Hi,

We just upgraded our OMERO server from 5.4.4 to 5.4.6. Since the upgrade, we cannot access images with a file name with accented character (é, è...). On Omero web, we can see the thumbnail but when opening the image with the image viewer, we get this error: "Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/user/.../Lame_094 - Épithélium nasal (40X).czi"

If I try to open it with iViewer, the image never show and when trying to download these images, i get this message: "Internal Server Error".

All other images (without accented characters) seems to work fine.

Is there anything we can do to fix this problem.

Thank you
Daniel

Hi Daniel,

sorry to hear about your problem. OMERO 5.4.6 contains an upgrade to Bio-Formats 5.8.2 which will force th reinitialization and the regeneration of memo files for each imported fileset. This will typically happen the first time an image is accessed following the upgrade.

Unfortunately the initialization time greatly varies from file format to file format. It is possible your Web error arises from the fact this memo file is regenerated. If you have access to the log files on the server, can you check whether you see a thread that read as:

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2018-05-16 20:48:43,730 INFO  [                loci.formats.ImageReader] (.Server-16) ZeissCZIReader initializing /opt/OMERO/OMERO.data/ManagedRepository/user/.../Lame_094 - Épithélium nasal (40X).czi


If the memo file is not regenerated after some time or you see an error in the server logs, we might need a sample file to be able to reproduce the issue.

Best,
Sebastien

Thank you for the answer,

We did some test on the server.

here is what we get with one of the file if we do a listing of the folder

Code: Select all

omero@omero3:~$ ls -al /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/
total 1510692
drwxr-xr-x 2 omero omero          3 May 10 14:18 .
drwxr-xr-x 8 omero omero         14 May 10 14:53 ..
-rw-r--r-- 1 omero omero 2387778560 May 10 14:22 Lame_002 - ?pith?lium pseudostratifi? cili?, trach?e (40X).czi


Here is a part of the log.

Code: Select all

Blitz-0.log:2018-05-16 10:09:38,356 ERROR [                ome.io.nio.PixelsService] (.Server-21) Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
Blitz-0.log:java.lang.RuntimeException: java.io.FileNotFoundException: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi (No such file or directory)
Blitz-0.log:Caused by: java.io.FileNotFoundException: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi (No such file or directory)
Blitz-0.log:2018-05-16 10:09:38,357 INFO  [        ome.services.util.ServiceHandler] (.Server-21)  Excp:   ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
Blitz-0.log:2018-05-16 10:09:38,357 INFO  [        ome.services.util.ServiceHandler] (.Server-21)  Excp:   ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
Blitz-0.log:2018-05-16 10:10:24,765 INFO  [        ome.services.util.ServiceHandler] (.Server-21)  Rslt:   ([{date=2018-05-10 14:22:44.909, sizeX=49653, name=Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi, ... 7 more}], [{date=2018-05-10 14:53:42.509, sizeX=106191, name=Lame_094 - Épithélium nasal (40X).czi, ... 7 more}], [{date=2018-05-10 14:20:00.196, sizeX=87480, name=Lame_097 - Trachée (sl) (40X).czi, ... 7 more}])
Blitz-0.log:2018-05-16 10:41:58,715 INFO  [             ome.io.nio.FilePathResolver] (.Server-27) Metadata only file, resulting path: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
Blitz-0.log:2018-05-16 10:41:58,718 ERROR [         ome.io.bioformats.BfPixelBuffer] (.Server-27) Failed to instantiate BfPixelsWrapper with /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
Blitz-0.log:2018-05-16 10:41:58,721 ERROR [                ome.io.nio.PixelsService] (.Server-27) Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
Blitz-0.log:java.lang.RuntimeException: java.io.FileNotFoundException: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi (No such file or directory)
Blitz-0.log:Caused by: java.io.FileNotFoundException: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi (No such file or directory)
Blitz-0.log:2018-05-16 10:41:58,722 INFO  [        ome.services.util.ServiceHandler] (.Server-27)  Excp:   ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
Blitz-0.log:2018-05-16 10:41:58,722 INFO  [        ome.services.util.ServiceHandler] (.Server-27)  Excp:   ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
Blitz-0.log:2018-05-16 11:57:44,108 INFO  [             ome.io.nio.FilePathResolver] (.Server-25) Metadata only file, resulting path: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
Blitz-0.log:2018-05-16 11:57:44,110 ERROR [         ome.io.bioformats.BfPixelBuffer] (.Server-25) Failed to instantiate BfPixelsWrapper with /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
Blitz-0.log:2018-05-16 11:57:44,113 ERROR [                ome.io.nio.PixelsService] (.Server-25) Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
Blitz-0.log:java.lang.RuntimeException: java.io.FileNotFoundException: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi (No such file or directory)
Blitz-0.log:Caused by: java.io.FileNotFoundException: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi (No such file or directory)
Blitz-0.log:2018-05-16 11:57:44,115 INFO  [        ome.services.util.ServiceHandler] (.Server-25)  Excp:   ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
Blitz-0.log:2018-05-16 11:57:44,253 INFO  [             ome.io.nio.FilePathResolver] (.Server-26) Metadata only file, resulting path: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
Blitz-0.log:2018-05-16 11:57:44,256 ERROR [         ome.io.bioformats.BfPixelBuffer] (.Server-26) Failed to instantiate BfPixelsWrapper with /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
Blitz-0.log:2018-05-16 11:57:44,260 ERROR [                ome.io.nio.PixelsService] (.Server-26) Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
Blitz-0.log:java.lang.RuntimeException: java.io.FileNotFoundException: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi (No such file or directory)
Blitz-0.log:Caused by: java.io.FileNotFoundException: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi (No such file or directory)
Blitz-0.log:2018-05-16 11:57:44,261 INFO  [        ome.services.util.ServiceHandler] (.Server-26)  Excp:   ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
Blitz-0.log:2018-05-16 11:59:32,523 INFO  [        ome.services.util.ServiceHandler] (.Server-27)  Rslt:   ([{date=2018-05-10 14:22:44.909, sizeX=49653, name=Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi, ... 7 more}], [{date=2018-05-10 14:53:42.509, sizeX=106191, name=Lame_094 - Épithélium nasal (40X).czi, ... 7 more}], [{date=2018-05-10 14:20:00.196, sizeX=87480, name=Lame_097 - Trachée (sl) (40X).czi, ... 7 more}])
Blitz-0.log:2018-05-16 14:07:06,368 INFO  [        ome.services.util.ServiceHandler] (.Server-25)  Rslt:   ([{date=2018-05-10 14:22:44.909, sizeX=49653, name=Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi, ... 7 more}], [{date=2018-05-10 14:53:42.509, sizeX=106191, name=Lame_094 - Épithélium nasal (40X).czi, ... 7 more}], [{date=2018-05-10 14:20:00.196, sizeX=87480, name=Lame_097 - Trachée (sl) (40X).czi, ... 7 more}])
OMEROweb.log:    serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
OMEROweb.log:    message = Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
OMEROweb.log:    serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
OMEROweb.log:    message = Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
OMEROweb.log:    serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
OMEROweb.log:    message = Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
OMEROweb.log:    serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
OMEROweb.log:    message = Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-32-24.946/Lame_094 - Épithélium nasal (40X).czi
OMEROweb.log:    serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
OMEROweb.log:    message = Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
OMEROweb.log:    serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
OMEROweb.log:    message = Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
OMEROweb.log:    serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
OMEROweb.log:    message = Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
OMEROweb.log:    serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi
OMEROweb.log:    message = Error instantiating pixel buffer: /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/Lame_002 - Épithélium pseudostratifié cilié, trachée (40X).czi


Looks like there is a problem with the filename.
His there a way to correct that.
Thank you for your help.
Daniel

Hi Daniel,

this is an interesting problem. The server logs at least suggest the problem is not at the level of the database.

dgarneau wrote:here is what we get with one of the file if we do a listing of the folder

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omero@omero3:~$ ls -al /opt/OMERO/OMERO.data/ManagedRepository/dgarneau_2/2018-05/10/14-18-18.080/
total 1510692
drwxr-xr-x 2 omero omero          3 May 10 14:18 .
drwxr-xr-x 8 omero omero         14 May 10 14:53 ..
-rw-r--r-- 1 omero omero 2387778560 May 10 14:22 Lame_002 - ?pith?lium pseudostratifi? cili?, trach?e (40X).czi


Although it might be a red herring related to the shell environment, the absence of accents in the file listing might very well be connected to the FileNotFoundException error thrown by the server.

Apart from the OMERO 5.4.4 to OMERO 5.4.6 upgrade, did anything change in the deployment environment of your server?
To help us troubleshoot your issue, two immediate questions come to our mind:

• what is the locale for the `omero` user on the server?
• is the managed repository mounted or the files in-place imported? And if so, what are the mount options?

Best,
Sebastien

Hi,

Nothing as changed on the server. We just upgraded OMERO.

Here is what we have for the locale

Code: Select all

omero@omero3:~$ env|grep -E "LC|LANG"
LC_ALL=en_CA.UTF-8
LANG=en_CA.UTF-8


for the last question, the system administrator sent me this:

Code: Select all

satapool/lxd-data/containers/omero on / type zfs (rw,relatime,xattr,noacl)

Can the problem come from the client used to send the images ?

Thank you,
Daniel

Dear Daniel,

That is an interesting question about the client used to send the images. In some local testing so far I've not managed to persuade a client to import such a file from a bad locale but I may not be trying the same workflows: for example, maybe it depends on a --transfer argument to OMERO.cli. Are these files with accented characters for images that did work before your upgrade?

The problem does look to be the mismatch between the ? on the filesystem and the accented characters that OMERO is expecting (based on the contents of the "name" column in the database's "originalfile" table) but nothing about the upgrade process from 5.4.4 to 5.4.6 should have changed this.

If you would like to upload a culprit file to http://qa.openmicroscopy.org.uk/qa/upload/ we could try doing a 5.4.4 to 5.4.6 upgrade at our end with your file imported -- with CLI or Insight, I wonder? -- to see if we can reproduce the problem but so far I do remain puzzled.

Cheers,
Mark

Hi,

Yes all the images were accessible before the upgrade.

We have rename the images on the server to change the "?" for the correct characters and we can now access the images on the client. So we could say problem solved for now.

The images were upload using Insight. I could send you a file but the smallest image is about 6.4 GB.

Thanks for the help.
Daniel

Dear Daniel,

Thank you for letting us know that renaming the files suffices as a workaround though I appreciate that it is hardly an ideal situation. If you have enormously many affected files then I may be able to help write an ad-hoc script to assist in the process. As even pre-upgrade images are affected I don't think it would help to obtain one of the actual images from you: locally in trying to reproduce the issue I have been testing with other, smaller ZEISS CZI files that I renamed to match that of yours.

I am afraid that I have no idea at all how the minor 5.4 version upgrade could have caused the problem that you experienced. The upgrade ought not affect existing files in the database or the binary repository nor can I find any relevant code changes that affect locale or character encoding. If anybody else in the community has seen anything like this apparently caused by a recent OMERO upgrade then I encourage them to let us know on this thread: maybe we can spot some common factor.

Cheers,
Mark