[Biojava-l] BioGroovy

Andy Yates ayates at ebi.ac.uk
Fri Aug 15 08:55:15 UTC 2008

Hi Mark,

There has been talk in the past about a groovier version of BioJava or 
at the very least showing where Groovy can help to reduce the verbosity 
of some parts of the biojava framework. I've done a tiny bit but my work 
has only been into prototyping Java code & quickly asserting some 
assumptions I had about BioJava (as in how the framework works).

What would be a brilliant step in a Groovier BioJava is to start 
levering the builders (http://groovy.codehaus.org/Builders). I mean 
imagine being able to write something like:

def myReferences = getReferences();

new EmblBuilder().build {
	myReferences.each{ ref ->
		reference {

I admit it's not a fully formed idea at the moment but hopefully you can 
see where I'm going with this :)

WRT Grails; our supported BioSQL API is written in Hibernate; just the 
same as GORM (Grails' ORM solution). So technically I cannot see a 
reason why it wouldn't be possible; my only wonder is how Grails 
controls transaction boundaries and translating this to our BioSQL.


Mark Fortner wrote:
> I've been using the biojava library with groovy lately and I ran
> across the BioGroovy.org site.  The site seems to be a placeholder and
> doesn't really have much information on it.  I was wondering if it was
> an official Bio* site?  Has anyone else been using Groovy (or any
> other scripting languages) with BioJava?
> Also has anyone looked at using Grails with BioSQL?  It would seem
> like an easy way to get something started quickly.
> Regards,

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