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Hi Niko,
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<div>assuming your server is still 5.0.5, you are likely hitting the same issue as the one reported in</div>
<div><a href="http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7673">http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7673</a>.</div>
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</div>
<div>You will need to pass the omero.db.pass via environment variable to be able to connect to the</div>
<div>database, i.e.</div>
<div><br>
</div>
<div>$ JAVA_OPTS="-Domero.db.pass=$(bin/omero config get omero.db.pass)" bin/omero admin reindex --reset 0</div>
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<div>After upgrade to 5.0.6 and later, this extra environment will no longer necessary since the password</div>
<div>is passed via environment variable in the CLI command directly.</div>
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<div>Let us know if this does not work,</div>
<div>Sebastien</div>
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<div>On 5 Feb 2015, at 17:20, Niko Ehrenfeuchter <<a href="mailto:nikolaus.ehrenfeuchter@unibas.ch">nikolaus.ehrenfeuchter@unibas.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Hi all,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Am I doing something wrong?<br>
<br>
Thanks a lot!<br>
~Niko<br>
<br>
<br>
[1] <a href="https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html">
https://www.openmicroscopy.org/site/support/omero5/sysadmins/search.html</a><br>
-- <br>
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel<br>
Phone: +41 (61) 26 72673 | <a href="mailto:nikolaus.ehrenfeuchter@unibas.ch">nikolaus.ehrenfeuchter@unibas.ch</a> |
<a href="http://www.biozentrum.unibas.ch">www.biozentrum.unibas.ch</a> | <a href="http://www.microscopynetwork.unibas.ch">
www.microscopynetwork.unibas.ch</a><br>
<span><re-index_error.log></span>_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br>
</blockquote>
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<br>
<div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
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</span></div>
</span></span></div>
<br>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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