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[bioontology-support] Programmatic migrations and Commands of the Virtual Appliance

Paul R Alexander palexander at stanford.edu
Tue Feb 4 17:50:28 PST 2014


> 1. Programmatic migrations script

We are planning to do this at some point, but it isn’t on our schedule yet and so I cannot commit to a timeframe.

If you’d like to do it yourself, here is how you can go about it:
GET http://data.bioontology.org/ontologies
For each ontology, get the latest submission (provided in the “links”)
For ontologies, overwrite the administeredBy list with user ids from users in the Appliance
Download the ontology file by following the download link: http://data.bioontology.org/{acronym}/download
POST the ontology metadata as JSON to http://{your_virtual_appliance}/ontologies
POST the submission metadata (including the file) as multipart/json to http://{your_virtual_appliance}/submissions
If you can use Ruby, then this library may be of use:
https://github.com/ncbo/ontologies_api_ruby_client/

I’m happy to answer questions regarding this process.

> 2. Command

I have just tried these commands and they work fine. You need to be logged in as the root user, though. Can you provide me with the exact error you are getting?

Thanks,
Paul


On Feb 3, 2014, at 11:38 PM, Jun-ichi Onami <onami at biosciencedbc.jp> wrote:

> Dear NCBO Support team,
> 
> Hi, We're planning to build bioportal mirror service with your new virtual
> appliance.
> I constructed this server on Xen virtual environment with your OVF file.
> 
> I have two questions.
> 
> 1. Programmatic migrations script
> 
> I found that programmatic migrations are currently unsupported.
> http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_migrate_ontologies_from_BioPortal_or_previous_NCBO_Virtual_Appliance_versions_into_a_new_Appliance.3F
> <http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_migrate_ontologies_from_BioPortal_or_previous_NCBO_Virtual_Appliance_versions_into_a_new_Appliance.3F>  
> 
> Do you have a plan to provide Programmatic migrations script like
> import_ontologies.rb utility in version1?
> If so, do you have a schedule for release it?
> 
> 2. Command
> 
> I tried to execute bpstart, bpstop, bprestart, and "/sbin/service 4store
> start" commands, suggested in  the wiki page
> <http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance#Basic_System_Administration> 
> .
> But these services/commands were unrecognized.
> 
> Do you have any reason for it?
> 
> 
> Sincerely,
> Jun-ichi Onami
> 
> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
> National Bioscience Database Center (NBDC)
> JAPAN SCIENCE AND TECHNOLOGY AGENCY (JST)
> JUNICHI ONAMI
> web: http://biosciencedbc.jp/en/
> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
> 
> 
> 
> --
> View this message in context: http://ncbo-support.2288202.n4.nabble.com/Programmatic-migrations-and-Commands-of-the-Virtual-Appliance-tp4652531.html
> Sent from the NCBO Support mailing list archive at Nabble.com.
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> bioontology-support at lists.stanford.edu
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