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

[Jerome Avondo]

Thanks Will,

That worked.

J.

________________________________
> CC: josh.moore at gmx.de; ome-users at lists.openmicroscopy.org.uk
> From: will at lifesci.dundee.ac.uk
> To: jeromeavondo at msn.com
> Subject: Re: [ome-users] OMERO 4.1.1 to 4.2.0 upgrade error...
> Date: Mon, 19 Jul 2010 15:31:57 +0100
>
> 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
>
> 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.
>
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> William Moore
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
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>
> Phone 01382 386364
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