[ome-users] Unhandled exception after migration

Wed Nov 19 20:00:31 GMT 2014

All appears to be working now. I did stop Omero, edit the file and then start Omero again. I updated the entries in the DB for the one file that I imported and it now works as well. Running the ‘select repo, count(*) from originalfile group by repo;’ query only reports the one repository like I would expect.

-Jason

From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: Wednesday, November 19, 2014 2:56 PM
To: Kotecki, Jason
Cc: OME Users
Subject: Re: [ome-users] Unhandled exception after migration

On Wed, Nov 19, 2014 at 5:24 PM, Kotecki, Jason <Jason.Kotecki at vai.org<mailto:Jason.Kotecki at vai.org>> wrote:

Hi Jason,

> Josh, I just imported an image and it looks like it uploaded to the new repository.
>
> select repo, count(*) from originalfile group by repo;
> Repo  Count
> ""    87
> "a652e6b8-be52-417e-b4d5-7921ffb93049"  6
> "ScriptRepo"  16
> "69b60b5f-cec8-42f6-8c33-668585685e61"  3894

That makes some sense. I'd also assume you see no issues with thumbnails, downloads, etc. From your previous mail:

The repo_uuid file contains:
^@$a652e6b8-be52-417e-b4d5-7921ffb93049

you can see that the new repository:

 4 | 5652 | a652e6b8-be52-417e-b4d5-7921ffb93049 | Managed | /omero_repo2/ManagedRepository

has become the ruler of this directory. I was hoping to find time to reproduce the steps today but didn't manage. After saving a copy of repo_uuid, my assumption is that if you stop OMERO, modify the UUID a652...049 to be:

  69b60b5f-cec8-42f6-8c33-668585685e61

and restart your server, that all the old images will start working, and the newly imported images will start failing. Then you can either delete those new test images, or update the files in the DB to also point to the old repository.

Cheers,
~Josh.

> -Jason
>
> -----Original Message-----
> From: Josh Moore [mailto:josh at glencoesoftware.com<mailto:josh at glencoesoftware.com>]
> Sent: Tuesday, November 18, 2014 8:35 AM
> To: Kotecki, Jason
> Cc: OME Users
> Subject: Re: [ome-users] Unhandled exception after migration
>
> Hi Jason,
>
> On Tue, Nov 18, 2014 at 3:13 AM, Kotecki, Jason <Jason.Kotecki at vai.org<mailto:Jason.Kotecki at vai.org>> wrote:
> > Here's the result of the "select repo, count(*) from originalfile group by repo" query.
> >
> > "";87
> > "69b60b5f-cec8-42f6-8c33-668585685e61";3894
> > "ScriptRepo";16
>
> So this says that only the original repository has any files, which is good. Could you also show us the contents of
>
>    /omero_repo2/ManagedRepository/.omero/repository
>
>
> Also, do you know if the original copy from the Windows server would have preserved the .omero directory?
>
> ~J.
>
>
> > -Jason
> >
> > -----Original Message-----
> > From: Josh Moore [mailto:josh at glencoesoftware.com<mailto:josh at glencoesoftware.com>]
> > Sent: Monday, November 17, 2014 5:43 PM
> > To: Kotecki, Jason
> > Cc: OME Users
> > Subject: Re: [ome-users] Unhandled exception after migration
> >
> > Hi Jason,
> >
> > On Nov 17, 2014, at 5:12 PM, Kotecki, Jason wrote:
> >
> >> ... In trying to troubleshoot this I came across this post: http://scanmail.trustwave.com/?c=129&d=8crr1A1ejF4P3raxq_th5UCbK6-b78ipRJtZbcr9-Q&u=https%3a%2f%2ftrac%2eopenmicroscopy%2eorg%2euk%2fome%2fticket%2f12355<http://scanmail.trustwave.com/?c=129&d=xfXs1L19ZaBiN3lsHWe-h60-UDhLFmJyA76c9Wcq7Q&u=https%3a%2f%2ftrac%2eopenmicroscopy%2eorg%2euk%2fome%2fticket%2f12355> Could the problem be similar to this?
> >
> > I think that's the same issue you're seeing. Could you run the SQL listed and send it to us?
> >
> >   select repo, count(*) from originalfile group by repo;
> >
> >
> > On Nov 14, 2014, at 6:21 PM, Kotecki, Jason wrote:
> >
> >> Mark, I was able to run the omero fs repos command once I realized that it needed an Omero user and not a linux user. Here is the output:
> >> # | Id   | UUID                                 | Type    | Path
> >> ---+------+--------------------------------------+---------+---------
> >> ---+------+--------------------------------------+---------+---------
> >> ---+------+--------------------------------------+---------+---------
> >> ---+------+--------------------------------------+---------+---------
> >> ---+------+--------------------------------------+---------+---------
> >> ---+------+--------------------------------------+---------+---------
> >> 0 | 1    | ScriptRepo                           | Script  | /home/omero/OMERO.server-5.0.5-ice35-b47/lib/scripts
> >> 1 | 2    | 69b60b5f-cec8-42f6-8c33-668585685e61 | Public  | /omero_repo2/ManagedRepository
> >> 2 | 3    | f06f1c35-1689-4283-ac0b-412f83a5cbd4 | Public  | /omero_repo2
> >> 3 | 5651 | 0d343001-6051-45a1-912e-659874f9d416 | Public  |
> >> /omero_repo2
> >> 4 | 5652 | a652e6b8-be52-417e-b4d5-7921ffb93049 | Managed |
> >> /omero_repo2/ManagedRepository
> >>
> >> It looks like it created a new managed repository ' a652e6b8-be52-417e-b4d5-7921ffb93049' but my other repository has a type of Public. How can I delete the new managed repository and change the type of my old repository?
> >
> > Going back to a previous thread:
> >
> >> Colin, thanks for the reply. The omero.data.dir is correct and I am able to open all of the images. I just can't download them. One thing I had to do to the database was to update the paths in the pixels and originalfile tables to switch the slashes from \ to /.
> >
> >
> > I'm wondering if the OMERO logic for detecting repo equality is breaking on some of these modifications. Could you try to reconstruct the steps to date so we can try to reproduce? For example:
> >
> >  * installed under Windows with omero.data.dir = C:\omero\data
> >  * moved to Linux; set omero.data.dir = /omero/data
> >  * executed SQL ...
> >
> > Cheers,
> > ~Josh.
> >
> >
> >> Thanks,
> >> Jason
> >>
> >> -----Original Message-----
> >> From: ome-users
> >> [mailto:ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>] On Behalf Of
> >> Mark Carroll
> >> Sent: Friday, November 14, 2014 10:44 AM
> >> To: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
> >> Subject: Re: [ome-users] Unhandled exception after migration
> >>
> >> Dear Jason,
> >>
> >> Are there any clues in your Blitz-0.log on the server when you try the failed download or the omero fs repos login? We would certainly be happy to help you diagnose any complaints from that log. I am coming to this thread a little late, but useful information in general may be:
> >>
> >> - Blitz-0.log extracts when wrong things happened
> >> - output of bin/omero admin diagnostics
> >> - any other information on how the server is configured (e.g. from
> >> bin/omero config get, but don't include any passwords!)
> >> - lines from the originalfile DB table or other relevant tables for the problem repositories and images, and any comments about how the paths and names in the table correspond to how the files on your actual disks are arranged.
> >>
> >>> I'm suspicious of the name '
> >> PublicRepository-69b60b5f-cec8-42f6-8c33-668585685e61'.
> >> '69b60b5f-cec8-42f6-8c33-668585685e61' is my ManagedRepository. Looking at the repositories in the 'originalfile' table of the database, I do not see a PublicRepository. Should there be one?
> >>
> >> This part is probably okay, at least: ManagedRepository is a subclass of PublicRepository, and it uses various methods from that class. It would also be good to make sure from psql that the output of this makes sense:
> >>
> >> select path from originalfile where name = 'ManagedRepository' and
> >> mimetype = 'Repository';
> >>
> >> If it is most convenient for you, feel free to risk sending too much
> >> information instead of too little: you can zip it all up and upload
> >> it via
> >> http://scanmail.trustwave.com/?c=129&d=8crr1A1ejF4P3raxq_th5UCbK6-b78
> >> ipRJRbPMmu-Q&u=http%3a%2f%2fqa%2eopenmicroscopy%2eorg%2euk%2fqa%2fupl
> >> oad%2f
> >>
> >> In the future, we are thinking that we really ought to write further documentation regarding moving OMERO's binary repository, as it can be tricky. Thank you for your patience as things are now!
> >>
> >> Have a good weekend.
> >>
> >> Cheers,
> >>
> >> Mark
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