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

Paul R Alexander palexander at stanford.edu
Mon Jun 18 16:10:57 PDT 2012


Does the call below return appropriately?
/bioportal/concepts/10001/root

Paul


On 6/18/12 3:18 PM, Madani,Sina wrote:
> 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.
>
>
> Sina
>
>
>
> On Jun 18, 2012, at 4:35 PM, "Paul R Alexander" 
> <palexander at stanford.edu <mailto:palexander at stanford.edu>> wrote:
>
>> 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 ..
>>>
>>>
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>

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