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[bioontology-support] 0.5 appliance loading error for SNOMED

Madani,Sina AHMadani at mdanderson.org
Mon Apr 30 08:28:27 PDT 2012


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?




[cid:image001.png at 01CD26BB.FB2F8DF0]


Thanks!
Sina

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