Images in viewer different from corresponding thumbnailss

[mtbc]

Dear Philippe,

Ah, we appreciate the difficulty, good luck with getting that information.

In the meantime: Apart from thumbnails, imports are working fine for you. Have you also tried importing plates, or just images? I just wondered if plates are importing correctly too and it is still only their thumbnails that are wrong. If you don't import plates, that's fine, don't worry about trying to get one from somewhere.

Cheers,
Mark

[PhilippeP]

Dear all,

In response to the plate import question: I cannot say, we only import images.

Concerning the thumbnail problem:
The colleague who took care of the reinstall just came back.
What was done is:

Ubuntu 16.04 freshly reinstalled
OMERO reinstalled (5.2, our last running version)
Postgres database restored from our last backup
OMERO 5.2 ->5.3->5.4 upgrade.

The output of the two queries are:

tiro_database=# SELECT id FROM thumbnail ORDER BY id DESC LIMIT 1;
id
--------
616383
(1 row)

tiro_database=# SELECT ome_nextval('seq_thumbnail');
ome_nextval
-------------
616432
(1 row)

I hope that helps understanding the thumbnails mismatch mystery.

[manics]

Hi Philippe

Are you absolutely sure the time of the last database backup is the same as the last change to the OMERO data dir?

[PhilippeP]

Hi Manics,

My understanding is that after our crash we (actually I) completely wiped the server sda disk clean for a fresh Ubuntu 16.04 reinstall, but not sdb1, which contains /OMERO and data. My colleague from the computer department tells me he did not have to restore /OMERO but reinstalled OMERO 5.2 (the version that was installed when the crash occurred) in sda home/omero, and resynchronized (? not sure what it means...) our data from the backup. We then did the upgrade 5.2->5.3, then 5.3->5.4.

[manics]

Hi Philippe

The most likely cause for the mismatch between the thumbnails and the images is a discrepancy between your OMERO data directory and the PostgreSQL database. OMERO caches the thumbnails, so for example if you were to inadvertently restore an older copy of your OMERO database, then any newly imported images would have the incorrectly cached thumbnails. Can you speak to your colleague and figure out whether this is a possibility?

[PhilippeP]

Hi Manics,

Thank you for your follow up.

I just discussed with Serge, who did the our database restoration. He says there may indeed be a difference in date between the base he restored and and the data directory.
He wants to know if there is a way to regenerate the database information from the data present in the /OMERO data directory, in order to solve the discrepancy between thumbnails and newly imported images?

And for my personal information, despite the proven fact that I am not that bright with programming could you explain in simple terms how come the thumbnails are not "simply" produced from the newly uploaded images instead of using cached thumbnails?

[manics]

Hi Philippe

Unfortunately these is no way to regenerate your database from the OMERO data directory. It should be possible to modify the OMERO data directory to match the database though, let us know if you'd like help with this.

[PhilippeP]

Thanks Manics,
Yes we sure would like help to modify the OMERO data directory to match the database!

[mtbc]

Dear Philippe,

Having the server's binary repository desynchronized with the database is very much an "undefined behavior" situation from our point of view. One theory is that maybe you have files in your server's "Thumbnails/" directory that do not have a corresponding ID in the database's "thumbnail" table but when the server comes to create the thumbnail file it finds there is already one.

In this case, a good approach may be to simply delete all the thumbnails on your system. When users view data the thumbnails will be regenerated so on a first viewing they may take a little while to appear.

You can do this using OMERO.cli, something like,

Code: Select all

$ bin/omero login   # as a full administrator, like "root"
...
$ bin/omero hql --style=plain --all --limit=-1 "SELECT id FROM Thumbnail" | sed -e 's!.*,!bin/omero delete Thumbnail:!' >/tmp/delete-thumbnails.sh
...
. /tmp/delete-thumbnails.sh


Cheers,
Mark

[mtbc]

Dear Philippe,

I should add, it may be a good idea to take a look at,

Code: Select all

bin/omero admin cleanse -h


Initially with the help of "--dry-run" you could investigate if other file-based mismatches could be cleaned up automatically using this "cleanse" subcommand.

Good luck,
Mark