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[bioontology-support] NCBO Virtual Appliance: can't connect with Protege

Ray Fergerson ray.fergerson at stanford.edu
Wed Sep 25 19:28:46 PDT 2013


David,



First you need to make sure that you are using Protégé 3.X rather than
4.X. The protégé database used by BioPortal (and the VM) is a 3.X version.



The Protégé/MySQL database user and password that you need are from here:



Configuration file
:/srv/ncbo/src/config/bioportal_core/build.properties.master.1056



This file has the following stuff:



protege.jdbc.url=jdbc:mysql://localhost/bioportal_protege?useUnicode=true&
amp;characterEncoding=UTF-8&holdResultsOpenOverStatementClose

=true

protege.jdbc.driver=com.mysql.jdbc.Driver

protege.jdbc.username=bp_protege

protege.jdbc.password=bioportalprotege





Ray



From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Johnson, David
Sent: Monday, September 23, 2013 6:26 AM
To: support at bioontology.org
Subject: [bioontology-support] NCBO Virtual Appliance: can't connect with
Protege



Hi,



I'm trying to follow the instructions under 'How do I add or change
categories?' from the FAQ
(http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ), however
I can't seem to get Protégé to connect to my VM's database. I get a
'RuntimeException. Message: Communications link failure', and it seems I
can't even telnet onto the MySQL port that I should be connecting to.



Is the VM configured in a particular way that blocks connecting from
outside?



I've tried looking for more comprehensive documentation on managing my own
instance of BioPortal (e.g. How to load/unload ontologies as an
administrator) but not found much apart front the wiki pages – a pointer
to some docs would be a great help.



Best/David

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