Open Microscopy Environment

Hi Blair,

the PR reported by Dominik above is definitely included in the 5.1.0 release. From our testing, I would expect it to solve your Blitz log issues after you have upgraded.

Best,
Sebastien

Great, thanks! I will update to 5.1.0 to see how things go.

I just attempted the update to 5.1.0, and most everything seems to be running fine. However, I am encountering Blitz log errors that may be related to this thread. Whenever I click on a thumbnail in the webclient, the following errors are created:

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2015-04-02 15:33:08,128 ERROR [                   loci.formats.Memoizer] (l.Server-1) deleting invalid memo file: /OMERO/BioFormatsCache/OMERO/ManagedRepository/brossetti_3/2015-01/09/11-43-59.129/.samplename.czi.bfmemo

I also get the following warnings:

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2015-04-02 15:33:08,937 WARN  [              ome.xml.model.OMEModelImpl] (l.Server-1) ome.xml.model.Channel@579e8e6e reference to null missing from object hierarchy.
2015-04-02 15:33:08,937 WARN  [              ome.xml.model.OMEModelImpl] (l.Server-1) ome.xml.model.Channel@4f414fdb reference to null missing from object hierarchy.
2015-04-02 15:33:08,937 WARN  [              ome.xml.model.OMEModelImpl] (l.Server-1) ome.xml.model.Channel@48a61000 reference to null missing from object hierarchy.
2015-04-02 15:33:08,937 WARN  [              ome.xml.model.OMEModelImpl] (l.Server-1) ome.xml.model.Channel@1139d7 reference to null missing from object hierarchy.
2015-04-02 15:33:08,937 WARN  [              ome.xml.model.OMEModelImpl] (l.Server-1) ome.xml.model.Channel@7f9e2437 reference to null missing from object hierarchy.
2015-04-02 15:33:08,938 WARN  [              ome.xml.model.OMEModelImpl] (l.Server-1) ome.xml.model.Channel@738ed773 reference to null missing from object hierarchy.
2015-04-02 15:33:08,975 WARN  [                      omero.cmd.SessionI] (l.Server-3) Servant already removed: e77d8bd4-6d2f-4e82-85e8-3a8edb53d269omero.api.ThumbnailStore

I uploaded my log here: https://www.openmicroscopy.org/qa2/qa/upload/

Do we think this might be related to the previous errors or is this something new resulting from a mistake in my upgrade?

Thanks,
Blair

Hi Blair,

the first ERROR you posted is expected as described in this section of the server upgrade. Post-upgrade, each memo file will be invalidated and re-created at first access. If you try to re-access the same image later, you should see no more ERROR in the logs related to memo file invalidation.

We will look at your second error and your uploaded logs and get back to you as soon as possible.

Best
Sebastien

Hi Blair,

after second thoughts, the `WARN` errors you reported above may also be related to the upgrade. Because of the modifications made to this particular reader in 5.1.x, there may be a mismatch between the objects read by Bio-Formats and the objects stored in the database. Would it be possible to upload the sample czi file to https://www.openmicroscopy.org/qa2/qa/upload/ for us to test the upgrade workflow?

Best,
Sebastien

Hi Sebastien,

Thanks for pointing out the memoization error! I need to read the documentation a bit more carefully I just uploaded one of the spectral czi files corresponding to the WARN errors. Please let me know if you would like any additional sample data.

Thanks!
Blair

Hi Blair,

thanks for the file upload. I was able to reproduce the WARN statements, by:

• importing the sample CZI file under 5.0.8, upgrading the server o 5.1.0 and trying to access the file
• importing the sample CZI file under 5.1.0: WARN statements are thrown in the server logs at import time
• manually deleting the BioFormatsCache folder of the 5.1.x server and trying to access the CZI file

In other terms, these warnings are not specific to the 5.0.x -> 5.1.0 upgrade but rather initiated by the call to `FormatReader.setId` on a CZI file when either there is no memo file or the memo file is invalidated. This may be due to a mismatch between the Bio-Formats reader and the OMERO model for some components of the model for this file file format. We will further investigate the issue and likely create a ticket for the 5.1.x milestone since we already have some CZI fixes planned. Let us know if you want to be cc'ed on the ticket.

Best,
Sebastien

Thanks for looking into this Sebastien! It would be great to be cc'ed on the ticket. Please let me know if I can provide any more information/files to help.

Cheers,
Blair

Thanks again, Blair. We're testing a fix for the warning messages now:

https://github.com/openmicroscopy/bioformats/pull/1714

I would expect this fix to be included in 5.1.1. Note that these warnings are not fatal, and shouldn't have an impact on importing or viewing the images. If you notice otherwise though, please let us know and we'll investigate further.

Regards,
-Melissa