[ome-users] OMERO 4.1.1 to 4.2.0 upgrade error...

[Will Moore]

Hi Jerome,

I'm going to try and answer for Josh, since he's actually on holiday  
right now (still checking his e-mail occasionally).

It looks like your user (id=2) is the owner of several Projects,  
Datasets and Images in group=2 ("default") but these have various  
links and annotations that were created in group=4 ("CoenLab").

You should be able to resolve these using the
omero-4.1-move-to-group.sql
script mentioned and linked from here:  http://openmicroscopy.org/site/support/omero4/server/db-upgrade-41-to-42

You can choose to move all of the data belonging to user=2 to either  
group 2 or 4.
E.g. to move to group 4, the command would be

psql -vGRP=4 -vUSR=2 -f omero-4.1-move-to-group.sql <my-database>

Then you should be able to upgrade 4.1 -> 4.0 as normal.
Just make sure you back up your DB, before you go ahead.

If you need reminding who is user ID=2, you can do
bin/omero user list

If the above solution doesn't fit your needs, then let us know (Josh  
will certainly have to handle that one).

  Hope this helps,

    Will.



On 19 Jul 2010, at 13:48, Jerome Avondo wrote:

>
> Hi Again,
>
> By manually editing I got a little further, but still stuck...
> Upgrade2.log file is attached, as well as the output from the  
> consolle (consolle.txt)
>
> thanks,
>
> J.
>
> ----------------------------------------
>> From: jeromeavondo at msn.com
>> To: josh.moore at gmx.de
>> Date: Mon, 19 Jul 2010 12:17:25 +0000
>> CC: ome-users at lists.openmicroscopy.org.uk
>> Subject: Re: [ome-users] OMERO 4.1.1 to 4.2.0 upgrade error...
>>
>>
>> Cheers Josh,
>>
>> Platform: CentOS 5
>> Postgresql: 8.1.11
>>
>> J.
>>
>> ----------------------------------------
>>> Date: Mon, 19 Jul 2010 14:07:53 +0200
>>> Subject: Re: [ome-users] OMERO 4.1.1 to 4.2.0 upgrade error...
>>> From: josh.moore at gmx.de
>>> To: jeromeavondo at msn.com
>>> CC: ome-users at lists.openmicroscopy.org.uk
>>>
>>> Jerome,
>>>
>>> What platform is this and what version of PostgreSQL? What's  
>>> happening
>>> is that the setting of the variable at the top of the upgrade  
>>> script:
>>>
>>> http://trac.openmicroscopy.org.uk/omero/browser/branches/Beta4.2/sql/psql/OMERO4.2__0/OMERO4.1__0.sql#L18
>>>
>>> is somehow losing its quotation marks on your platform and being
>>> interpeted as: \set ACTION ABORT
>>>
>>> It'd be good to fix this for others, but if you would like to move
>>> forward you can change the use of ":ACTION" here:
>>>
>>> http://trac.openmicroscopy.org.uk/omero/browser/branches/Beta4.2/sql/psql/OMERO4.2__0/OMERO4.1__0.sql#L542
>>>
>>> to say:
>>>
>>> select * from omero_41_check1(cast('ABORT' as text));
>>>
>>> Cheers,
>>> ~Josh
>>>
>>> On Mon, Jul 19, 2010 at 11:20 AM, Jerome Avondo wrote:
>>>> This is the error I get on the command line:
>>>>
>>>> psql:OMERO4.1__0.sql:542: ERROR: column "abort" does not exist at  
>>>> character
>>>> 36
>>>> psql:OMERO4.1__0.sql:542: LINE 1: select * from  
>>>> omero_41_check1(cast(ABORT
>>>> as text));
>>>> psql:OMERO4.1__0.sql:542: ^
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> J.
>>
>> _________________________________________________________________
>> http://clk.atdmt.com/UKM/go/197222280/direct/01/
>> Do you have a story that started on Hotmail? Tell us now
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> 		 	   		
> _________________________________________________________________
> http://clk.atdmt.com/UKM/go/195013117/direct/01/
> < 
> upgrade2 
> .log><consolle.txt>_______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
http://openmicroscopy.org.uk




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20100719/67a805c6/attachment.html>