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[bioontology-support] loaderBigConcepts issue in Annotation services (applaince 0.5)

Madani,Sina AHMadani at
Mon Jun 18 15:18:15 PDT 2012

Hi Paul,

Few hours (at least 8) The ontology is very small (<400 terms).
The appliance 0.4 version finished both concept and path processes and changed status in half an hour.


On Jun 18, 2012, at 4:35 PM, "Paul R Alexander" <palexander at<mailto:palexander at>> wrote:


This step can take a very long time to complete depending on the size of the ontology. How long have you let it run at this stage?

Paul R Alexander
Senior Software Engineer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research

On 6/14/12 8:40 AM, Madani,Sina wrote:


I just added a small ontology to the Annotation services in our local 0.5 instance. At the "loaderBigConepts" step, the status starts from 11 (after successful check of initial status of 3) but remains at status 12.
The last three lines of catalina log is pasted below. After "pagenum 5"  I am getting a strange "Roots...." message

I was able to add the same ontology into 0.4 annotation instance though. The loaderBigConcepts successfully finishes with status 14 and then loaderBigpaths works it to status 28.
This could be a possible bug in version 0.5?


INFO: 2012-06-14     03:09:01     -     8080   GET       /bioportal/concepts/10001/all      pagenum=4&pagesize=500&apikey=11111111-9dd1-11e0-a996-115056bd0024  200    5677709       0      1748   http://localhost:8080       BioPortal-OBS -
Jun 14, 2012 3:09:04 AM org.restlet.engine.log.LogFilter afterHandle
INFO: 2012-06-14     03:09:04     -     8080   GET       /bioportal/concepts/10001/all      pagenum=5&pagesize=500&apikey=11111111-9dd1-11e0-a996-115056bd0024  200    517999 0      117    http://localhost:8080       BioPortal-OBS -
Jun 14, 2012 3:09:07 AM org.restlet.engine.log.LogFilter afterHandle
INFO: 2012-06-14     03:09:07     -     8080   GET       /bioportal/concepts/10001/root     apikey=11111111-9dd1-11e0-a996-115056bd0024      200    14445  0       56     http://localhost:8080       BioPortal-OBS -

       Roots ..

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