[Biojava-l] Running apps with Java

[Keith James]

>>>>> "Thomas" == Thomas Down <thomas at derkholm.net> writes:

[...]

    Thomas> Yes, I quite agree.  Although I think I'd prefer something
    Thomas> more like:

    Thomas>    params.addParameter(NCBIBlast.PROGRAM_NAME, "blastn")

    Thomas> Have you looked at the AnnotationType class?  We could
    Thomas> probably use those to do the parameter set validation.

IMO having program names hardcoded in the method names or even as
parameters greatly increases the amount to code required for a typical
system. A public exec method per program will result in a lots of
methods and requires rebuilding the jars to deploy a new external
program (same with static parameters specific to a program).

Having a single, generic exec method with a means of discovering local
native programs is simpler and more maintainable. This can be done
simply with ResourceBundles (which also means that one can
internationalize for free)

e.g.

NCBIBlast_en_GB.properties

-p = String : Program name
-d = String : Database, default = nr
-i = String : Query file, default = stdin
-e = Double : Expectation value (E), default = 10.0

etc.

NCBIBlast_fr.properties

-p = String : Nom de programme

etc.

I think it is important to allow end users to configure their biojava
to run their native applications without writing any code.

    Thomas> The other big win would be to do something at least
    Thomas> vaguely sane about finding executables.  Hardcoded paths
    Thomas> aren't a problem if you are running on your own machines,
    Thomas> but if people want to deploy BioJava-based applications
    Thomas> widely, they really need to be able find blast on their
    Thomas> own...

You can do this simply by adding a key/value to the resouce giving the
full path. Alternatively this keyed value could be the name of a JNDI
resource etc. for situations which require it.

I've been running a simple Java-based workflow & execing system in
anger for the past year (lots of different native programs) and native
program maintenance requiring rebuilding production of jar files is
not something I'd want to deal with.

cheers,

Keith

-- 

- Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -