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

Paul R Alexander palexander at stanford.edu
Mon Jun 18 14:33:41 PDT 2012


Sina,

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:
>
> Hi,
>
> 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?
>
> Thanks
>
> Sina
>
> INFO: 2012-06-14     03:09:01      127.0.0.1     - 127.0.0.1     
> 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      127.0.0.1     - 127.0.0.1     
> 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      127.0.0.1     - 127.0.0.1     
> 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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> bioontology-support at lists.stanford.edu
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