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[bioontology-support] Enabling cron job in VA

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Sep 6 10:34:03 PDT 2017


Hello Line,


On Sep 6, 2017, at 7:57 AM, Pouchard, Line <pouchard at bnl.gov<mailto:pouchard at bnl.gov>> wrote:

Dear all:

Can you please send directions on how to enable a cron job for automatic update of ontologies in the Virtual Appliance?


I’m not sure I understand exactly what you’re asking. The BioPortal Virtual Appliance comes with a project called ncbo_cron that contains a background task that checks the ontology parsing queue for new ontologies every 5 minutes. If you add a new ontology submission, the parsing process should begin within 5 minutes. The ncbo_cron background task is automatically launched when you install the Virtual Appliance, so there shouldn’t be any additional steps necessary on your part.

Or, perhaps you’re referring to the desire to enter a URL for an ontology that’s checked nightly for new submissions? If so, this is something you configure yourself when you add a new ontology submission. On any ontology summary page, you can click the "Add submission" link, and enter such a pull URL in the Location section of the resulting form:


[cid:BC9811AA-3FF7-4FA6-957A-20843FCC571F at hsd1.ca.comcast.net]


Choose the “Load from URL” radio button, and enter the URL that points to your ontology source file. Once you’ve filled out this form and click the “Add submission” button, the Virtual Appliance will pull the initial version of your ontology from that URL, and it will also begin checking on a nightly basis for new versions. If a new version is detected, it will automatically get downloaded/processed.

Hope that helps.

Kind regards,
Jennifer

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