[Biojava-dev] RE: New RDBMS support: hsqldb

[Len Trigg]

Mark Schreiber wrote:
> Either is probably OK, depends on the size of the jar I suspect. If
> its a big hit to download then I suppose we can make it an optional
> part of the ANT build.

I've committed the unit tests and the biosql schema files I ported. I
have not added the hsqldb jarfile - people wanting to run these tests
need to download it (I am using the stable 1.7.1 release - there is a
problem with the current bleeding edge version, so don't use that) and
add it to their classpath before executing the tests. If you don't
have the driver in your classpath, the tests are skipped, e.g.:

    [junit] Running org.biojava.bio.seq.db.HashSequenceDBTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Time elapsed: 5.273 sec
    [junit] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest
    [junit] No hsqldb driver found.
    [junit] Tests run: 0, Failures: 0, Errors: 0, Time elapsed: 0.008 sec

 
I found and fixed a bug in BioSQLAllFeatures.java. The bug also exists
in BioSQLTiledFeatures.java, but I don't understand what that code is
doing -- if someone could take a look at it, it'd be appreciated. To
trigger it, the easiest way is to run the unit tests after editing
BioSQLSequence.getFeatures() to always use BioSQLTiledFeatures rather
than only using that implementation for long sequences.

Cheers,
Len.