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[bioontology-support] Few VA related questions

Darren Weber dlweber at stanford.edu
Mon Mar 24 10:56:32 PDT 2014


On 3/20/14, 8:55 AM, Clement Jonquet wrote:
>
> Hi all,
>
> We have been starting to use our local VA and getting ready to change 
> the Annotator code inside.
>
> We have a few questions for which answers ca save us long time ;) :
>
> 1.Where do you suggest to check out the code from at the beginning ? 
> From the NCBO GitHub or directly from the VA files? For instance, if 
> we want to change the \bioportal_web_ui project to update the UI of 
> our local BP. Should we get: https://github.com/ncbo/bioportal_web_ui  or
>
> /srv/rails/BioPortal/releases/bioportal_web_ui on the VA  or
>
> somewhere else ?
>
> The idea is to avoid any conflict if the code on GitHub is more recent 
> than the one executed on the VA.
>

Use github and git to mange source.  If you have minor changes, suggest 
patches to the main repo.  If you have major changes, fork it.  Manage 
everything with git (repos, branches, merges, etc.).

> 2.What do you guys use for automatic deployment from GitHub to stage 
> or production BP ? Maeven, or alike… any place we should look into on 
> the VA?
>

The ruby platform use rbenv with bundler to manage dependencies and 
capistrano to code deployment rules.  We use Jenkins to automate it.  A 
lot of deployment specific details are config parameters.

> 3.Where are we defining groups and categories for our ontologies ?
>
> 4.Is there an admin interface (more advanced that the admin login) 
> that enable to see what’s going on with the parsing of ontologies.. 
> i.e., where to look if the parsing of an ontology fails to clean up or 
> debug. Maybe also define groups, etc.
>
> 5.Where should we look if we want to change what’s happening 
> automatically when an ontology is added to BP via the UI. We 
> specifically are interested in the MGREP dictionary creation step that 
> we want to separate by “group”… in order to create/update a group 
> specific dictionary file (in order for us to have 2 annotator on the 
> same VA) ?
>

Ontology submission is managed in the REST API [1], look at the 
code/logs there.  It is also managed by the ncbo_cron project [2], look 
at the code/logs there.

[1]  https://github.com/ncbo/ontologies_api
[2]  https://github.com/ncbo/ncbo_cron


Hope that helps,
Darren


> Thank you by advance J
>
> Clement, Emmanuel and Soumia
>
> ---------------------------------------------------------------------------------------------------------------------------
>
> Dr. *Clement JONQUET*  - /PhD in Informatics  -  Assistant Professor/
>
> /PI of the SIFR project <http://www.lirmm.fr/sifr/>: Semantic Indexing 
> of French Biomedical Data Resources (ANR, UM2, CNRS, IBC)/
>
> /Organizer of Web Science Montpellier 
> <http://www.meetup.com/webscience-montpellier/> Meetup/
>
> jonquet at lirmm.fr <mailto:jonquet at lirmm.fr>
>
> http://www.lirmm.fr/~jonquet <http://www.lirmm.fr/%7Ejonquet>
>
> *University of Montpellier* Tel:                      +33/4 67 14 97 43**
>
> LIRMM                                                            Fax: 
>         +33/4 67  41 85 00
>
>                 161 rue Ada 
>                                                   Skype:        clementpro
>                 34095 Montpellier Cdx 
> 5                            Twitter: @jonquet_lirmm 
> <http://twitter.com/jonquet_lirmm>
>
> France                                                            Google: 
> jonquet.lirmm at gmail.com <mailto:jonquet.lirmm at gmail.com>
>
> ----------------------------------------------------------------------------------------------------------------------
>
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