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

[Niko Ehrenfeuchter]

Hi all,

just to let you know, re-indexing the database solved our search issues, 
at least as far as we can tell for now (in other words, everything that 
we expected to show up is actually there right now).

For the record, the indexing of our current ~19 TB binary repository 
took 8h 36m in background (on-line) mode. That's much much faster that I 
was expecting from reading the documentation [1].

Thanks again!
~Niko

[1] 
https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html#monitoring-re-indexing



On 06.02.2015 10:13, Niko Ehrenfeuchter wrote:
> 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