[ome-users] Re-indexing OMERO's search database

[Niko Ehrenfeuchter]

Hi Sebastien,

thanks for the very quick reply. Indeed, we are still on 5.0.5 as I 
mentioned in another email (thanks for the sharp reading!) and your hint 
solved this problem. Re-indexing is now in progress.

Thanks again!
~Niko

On 05.02.2015 21:31, Sebastien Besson (Staff) wrote:
> Hi Niko,
>
> assuming your server is still 5.0.5, you are likely hitting the same
> issue as the one reported in
> http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7673.
>
> You will need to pass the omero.db.pass via environment variable to be
> able to connect to the
> database, i.e.
>
> $ JAVA_OPTS="-Domero.db.pass=$(bin/omero config get omero.db.pass)"
> bin/omero admin reindex --reset 0
>
> After upgrade to 5.0.6 and later, this extra environment will  no longer
> necessary since the password
> is passed via environment variable in the CLI command directly.
>
> Let us know if this does not work,
> Sebastien
>
> On 5 Feb 2015, at 17:20, Niko Ehrenfeuchter
> <nikolaus.ehrenfeuchter at unibas.ch
> <mailto:nikolaus.ehrenfeuchter at unibas.ch>> wrote:
>
>> Hi all,
>>
>> we're experiencing some odd behaviour of the search functionality in
>> OMERO recently, by missing many files when doing a search. So I went
>> and checked the docs [1] for this, making sure the Indexer is neither
>> stuck nor running behind.
>>
>> After checking this, I thought I will "just" do a (background)
>> re-indexing before I start bothering you again. However, from the
>> commands listed in the documentation, the third one (--reset 0) keeps
>> on failing. The output, including the stack traces can be found in the
>> attached log file.
>>
>> Am I doing something wrong?
>>
>> Thanks a lot!
>> ~Niko
>>
>>
>> [1]
>> https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html
>> --
>> Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum,
>> University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
>> Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch
>> <mailto:nikolaus.ehrenfeuchter at unibas.ch> | www.biozentrum.unibas.ch
>> <http://www.biozentrum.unibas.ch> | www.microscopynetwork.unibas.ch
>> <http://www.microscopynetwork.unibas.ch>
>> <re-index_error.log>_______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> <mailto:ome-users at lists.openmicroscopy.org.uk>
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> Dr Sébastien Besson
> Open Microscopy Environment / Harvard Medical School
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>

-- 
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University 
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch | 
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch