[Bioperl-l] PostgreSQL schema support in BioSQL and bioperl-db

[Richard Holland]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Sounds great.

BioJava users shouldn't need to change anything to get this to work as
PostgreSQL JDBC connection objects already require you to specify a schema.

cheers,
Richard


Hilmar Lapp wrote:
> I have added support to BioSQL and bioperl-db for schemas in PostgreSQL.
> A schema in PostgreSQL is more or less a namespace for database objects
> (tables, indexes, views, etc) within a database.
> 
> (A database in PostgreSQL is similar to the concept of a user in Oracle
> or MySQL, and therefore for the latter two schemas are synonymous with a
> user. [Not sure I'm still up-to-date on this for MySQL, but at least
> that's what I recall.])
> 
> When using the load_{seqdatabase,ontology,ncbi_taxonomy}.pl scripts, you
> specify the schema in which BioSQL resides using the --schema option.
> 
> If you are using bioperl-db as a library, the Bio::DB::BioDB->new() call
> also accepts a -schema named parameter, and Bio::DB::DBContextI objects
> have a $dbc->schema() property for getting/setting the schema,
> Bio::DB::SimpleDBContext->new() accepts a -schema parameter, and you may
> also add the property to the .bioperldb connection parameter file
> (-schema => 'yourschemahere').
> 
> Thanks for Brian Osborne for being the instigator (and tester, and for
> adding the code to load_ncbi_taxonomy.pl - I came too late).
> 
>     -hilmar
> --===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFGZ7TF4C5LeMEKA/QRApwUAJ48q46iX152pB6Xcc/717Ie8foUTQCgm3ij
W/+0iO/ZsNDn1pLuf5yXbYA=
=asUn
-----END PGP SIGNATURE-----