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

[Sebastien Besson (Staff)]

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>
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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
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