[Biojava-dev] BioSQL/Oracle

[Len Trigg]

Hi guys,

I have support for BioSQL with Oracle working (of a sort). I just
posted a message to the biosql list outlining the difficulties I had,
but to cut to the chase I just ported the mysql schema rather than
using the existing oracle biosql schema. From then on, adding BioJava
support for this was pretty simple. A summary of the changes:

In BioSQLSequenceDB.java, the various is*Supported methods had a lot
of common code that didn't work with Oracle, so I made most of them
use a containsTable() method. This method lives in the DBHelper so it
can be database specific.

I then made an OracleDBHelper class that handles getting the last
insert id and the custom method for detecting if a table exists.

This works with the schema I posted to the biosql list, but not the
existing oracle biosql schema (the table and field names are all
wrong). If this sounds OK, I'll commit it.


Cheers,
Len.