[DAS2] biopackages server UML

Brian O'Connor boconnor at ucla.edu
Tue Oct 10 22:51:54 UTC 2006

Hi Allen,

I have a few questions.

* How does feature (and other data types) filtering take place?  Does 
the controller passes info into read_features() in Das2::Model::Genome? 
  Where is the actual filtering implementation?  In 

* Where will the SQL queries live?  In the current implementation we 
have an object where many of the prepared statements live.  Do you plan 
on using something similar here?  Or will the SQL generally be embedded 
in Das2::Model::Record objects and Das2::Model::Genome::Chado?

* For the Das2::Model::Record subclasses, should there be another layer 
of inheritance with a Das2::Model::Chado::Record object?  In case you 
want additional data adapters for other DBs/flat files in the future?


Allen Day wrote:
> Hi,
> I'm attaching my first draft for the UML of a server rewrite.  Aside 
> from all the spec churn, there are two main types of requests that need 
> to be handled that spurred me to do this rewrite.  The third reason I'm 
> doing this is to rework the caching mechanism on the server.  With the 
> current code base there is a lot of custom table clustering and 
> denormalization to get decent performance out of the Chado database.  I 
> did some experimenting (discussed in an earlier thread and on conf. 
> calls) with a "tiling" or "block" caching strategy of cache that turns 
> out to work really well, and I wanted to integrate that with the 
> writeback functionality.
> 1) tighter integration of writeback, including locking.
> 2) configurability of feature types to be
>   * dynamic (e.g. for on-the-fly gene prediction)
>   * non-cacheable
>   * cacheable
> 3) caching
>   * segment range/type tiled caching
>   * ability of writeback events to trigger cache flush events
> See attached UML.  There is a .zuml file, you can view/edit with 
> Poseidon, or if you need a .xml I can send another attachment.
> -Allen
> ------------------------------------------------------------------------

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