[ome-users] Unhandled exception after migration

Tue Nov 18 14:09:28 GMT 2014

Here's the contents:

[omero at localhost 210e9d11-5f29-4faf-a5e4-4aeb09fd127b]$ ls -l
total 2
-rw-rw-r--. 1 omero omero 38 Nov 14 10:55 repo_uuid

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

-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com] 
Sent: Tuesday, November 18, 2014 9:06 AM
To: Kotecki, Jason
Cc: OME Users
Subject: Re: [ome-users] Unhandled exception after migration

On Tue, Nov 18, 2014 at 2:58 PM, Kotecki, Jason <Jason.Kotecki at vai.org> wrote:
> Josh, here's the listing of /omero_repo2/ManagedRepository/.omero/repository.
>
> [omero at localhost /]$ ls -la 
> /omero_repo2/ManagedRepository/.omero/repository/
> total 9
> drwxrwxr-x. 3 omero omero 3 Nov 10 11:39 .
> drwxrwxr-x. 3 omero omero 3 Nov 10 11:39 ..
> drwxrwxr-x. 2 omero omero 4 Nov 14 10:54 
> 210e9d11-5f29-4faf-a5e4-4aeb09fd127b

Could you send me the contents of this directory?

> Yes, the copy would have preserved all of the folders.

Great.

~J.

> Thanks,
> Jason
>
> -----Original Message-----
> From: Josh Moore [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> 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]
>> 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=ttLr1Py-UHixU2lpFJIc_kPzDHb0gySVObYF4-jCtQ&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] On Behalf Of 
>>> Mark Carroll
>>> Sent: Friday, November 14, 2014 10:44 AM
>>> To: 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-b7
>>> 8 
>>> ipRJRbPMmu-Q&u=http%3a%2f%2fqa%2eopenmicroscopy%2eorg%2euk%2fqa%2fup
>>> l
>>> 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