Re: [Gusdev-gusdev] GUS And Bioperl

[Steve F. <st...@pc...>]

Arnaud-

You can get a db connection without the plugin manager.  see 
$PROJECT_HOME/GUS/Common/bin/deleteEntries.pl for example.

But, as far as running plugins, that inherently involves the plugin 
framework.  If you are only reading the db, you won't need this.

Also, while mapping using the object layer may be easier, it may also be 
slower, possibly significantly (but this bears looking into).

steve

Arnaud Kerhornou wrote:

> Hi
>
> Following the conference call, I've been working on setting up a demo 
> about interfacing Bioperl and having GUS as a datasource. There are 
> several ways for doing this.
> * The first way is to implement the Bioperl-db interfaces to point at 
> GUS instead of a BioSQL database. That involves to map the GUS 
> relational design into the Bioperl one. It would be used in a 
> read-only mode.
> * A second way is to map Bioperl Objects into GUS objects and use the 
> GUS objects API to access the database. That seems to involve less 
> work  as the mapping between the object layer and the relational layer 
> as well as the DB connections would be delegated to the GUS layer. 
> This code could be used for read and write access.
>
> To do so, I've tried to use the GUS object layer, but it is actually 
> embedded into the Plugin Framework which processes the initialisation 
> step (DB connection, plugin registration...). How could I use the perl 
> layer independently of the GusApplication framework ?
>
> Thanks
> Arnaud
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: VM Ware
> With VMware you can run multiple operating systems on a single machine.
> WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines at the
> same time. Free trial click here: http://www.vmware.com/wl/offer/345/0
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev