[Biojava-l] Running apps with Java

[Schreiber, Mark]

I would tend to agree with Keith. Making hardcoded command lines can loose platform independence pretty quickly. I would prefer to see users register their own command lines, preferences etc with some kind of registry object.
 
- Mark
 

	-----Original Message----- 
	From: Keith James [mailto:kdj at sanger.ac.uk] 
	Sent: Tue 12/08/2003 10:46 p.m. 
	To: Thomas Down 
	Cc: biojava-l at biojava.org 
	Subject: Re: [Biojava-l] Running apps with Java
	
	

	>>>>> "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 -
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