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[bioontology-support] [POSSIBLE VIRUS:###] Re: 0.5 appliance loading error for SNOMED

Trish Whetzel whetzel at stanford.edu
Thu May 10 11:27:37 PDT 2012


Attached is the latest pre-processed version of NCIt.  The pre-processing step is mentioned in:
http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance#Population_Workflows 

Trish 





On May 10, 2012, at 11:06 AM, Madani,Sina wrote:

> Update:
> I was able to bypass the mentioned MYSQL problem by loading SNOMED using LexEVS514 GUI within our local appliance (0.5) and using the included lbconfig.props file (instead of using the appliance Admin utility). I guess I need to update manually some tables for SNOMED meta data.
>  
> Sina
>  
> From: Madani,Sina 
> Sent: Monday, April 30, 2012 10:28 AM
> To: support at bioontology.org
> Subject: 0.5 appliance loading error for SNOMED
>  
> Hi ,
>  
> Loading SNOMED into Bioportal V 0.5 went through until the end of indexing. But at the very last step I got below error and parsing failed (lexevs log file attached). Do you have any suggestion to fix this? I tried this twice and both times it failed at the very same step.
>  
> com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
>  
> Googling the error points to the issue of "netTimeoutForStreamingResults" for very large datasets...
>  
> Also, I am not sure if this is a related issue or not but I am getting the error shown in the screenshot below whenever I restart ncbo service.
> Is any of the MySQL parameters have been changed in the 0.5 appliance?
>  
>  
>  
>  
> <image001.png>
>  
>  
> Thanks!
> Sina
>  
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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