[BioSQL-l] Oracle support...

[Len Trigg]

Hilmar Lapp wrote:
> Where these would would be the 'comment' table and 
> term_synonym.synonym, right?

Yep.

> If you look at BS-create-Biosql-API you'll see that I aliased the 
> sg_comment table to anncomment. Also, in the Oracle version the column 
> term_synonym.synonym becomes term_synonym.name.
> 
> The latter I think should also be it's name in the mysql and Pg 
> versions because it would be consistent with the naming standard 
> introduced at the Singapore hackathon.
> 
> Same applies to the comment table.

I agree. Maybe there needs to be a TODO file (or section to README) in
CVS, that details changes scheduled to be made post-1.0 (which
hopefully won't be too many months away ;-)):

  - Rename comment table to anncomment and rename term_synonym.synonym
  to term_synonym.name in mysql and pg schemas.


> Is your Biojava/Oracle support for biosql able to handle names 
> different from the otherwise expected Pg schema?

No, the BioJava BioSQL support requires the names to be the same as
the pg/mysql schema (and it doesn't look like a small change to factor
that out). The RDBMS specific classes mainly just handle differences
in the RDBMS capabilities itself, rather than schema differences.


Cheers,
Len.