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

[Hilmar Lapp]

I guess I'm behind the curve here a bit - schemas are optional in  
Postgres - if you say JDBC connection objects require a schema, does  
that mean it may also be null or empty?

	-hilmar

On Jun 7, 2007, at 3:33 AM, Richard Holland wrote:

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> 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 :
>> ===========================================================
>>
>>
>>
>>
>>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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