[Bioperl-l] UCSC database backend
bix at sendu.me.uk
Thu Aug 10 02:56:59 EDT 2006
Sean Davis wrote:
> I have put together a variation of the database backend. It is based on
> DBIx::Abstract and exposes a bit more of the SQL and DBI. Since UCSC uses
> cross-database queries, it might be a better fit for the problem than an
> ORM. It is pretty simple, but I don't know that we need much more here.
> The harder problem, as I mentioned earlier, is to determine what to return,
> not how to return it. I am showing only a couple of the DBIx::Abstract
> methods here; there are a number of others for fetching data. In
> particular, pretty much any of the fetch_* are available.
Seems to be reasonable so far. You could probably use the
'introspection' calls to build other access methods on-the-fly.
> A fair bit of work on the connection end. In particular, I will
> bly make a "Bio::DB::SQL" class that encapsulates some methods for
> working with SQL databases and some kind of abstraction for
> information, making it easier to switch from local to remote versions
> of a database.
That sounds really interesting.
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