[Biojava-l] Bug fix for biojava class RichObjectFactory.java in current maven based project

[mark.schreiber at novartis.com]

Could a subclass of the RichObjectFactory exist in the BioSQL module. If 
you want your RichObjects backed by BioSQL you use the 
[BioSQL]RichObjectFactory from the BioSQL package???

- Mark


biojava-l-bounces at lists.open-bio.org wrote on 03/10/2010 09:31:43 PM:

> The problem is that the RichObjectFactory is generic, but the 
> connectToBioSQL method is BioSQL specific. What really needs to 
> happen is abstract out the connectToBioSQL method _only_ to a more 
> specific class in the biosql module, and use (if necessary create) 
> setters on RichObjectFactory for it to use.
> 
> 
> On 10 Mar 2010, at 04:10, Deepak Sheoran wrote:
> 
> > Hi Andreas
> > I guess it should go in "org.biojavax.bio.db.biosql" package, it 
> make sense to put this class their.
> > 
> > Deepak Sheoran
> > 
> > On 3/9/2010 11:28 AM, Andreas Prlic wrote:
> >> Hi Deepak,
> >> 
> >> thanks for spotting this. This factory method should clearly be 
> moved to the biosql module and not be part of the core.  Anybody who
> has a deeper knowledge of the biosql code: Where is the best place 
> in the biosql module to move this to?
> >> 
> >> A work around the compile problem would be to use reflection to 
> mask the calls to the methods in the other module, but it feels likea 
hack...
> >> 
> >> Andreas
> >> 
> >> On Mon, Mar 8, 2010 at 1:11 PM, Deepak Sheoran <sheoran143 at gmail.com 
<
> mailto:sheoran143 at gmail.com>> wrote:
> >> 
> >>    Hi
> >>    I was making a local version of current maven project on my
> >>    machine so that i can fix some reference related bugs in biojava.
> >>    But when I build the local version and tried to use it. I got an
> >>    error on method
> >>    RichObjectFactory.connectToBioSql(Object session) of current
> >>    version of bio-java live. when I had a look on it I saw a comment
> >>    on it
> >> 
> >>       "// commenting out for the moment, since it prevents core from
> >>    compiling.
> >>       // TODO: move to BioSql module"
> >> 
> >>    then I uncommitted the code and add these import statements to
> >>    RichObjectFactory.java and the problem is fixed :
> >> 
> >>    import org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver;
> >>    import org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder;
> >>    import org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler;
> >> 
> >>    After this I tried compiling bioSql module it went successfully
> >>    and also when I compiled Core module it went successfully too.I
> >>    don't if this is the only reason then please uncomment these line
> >>    in main svn version since i don't how to do it.
> >> 
> >>    Thanks
> >>    Deepak Sheoran
> >> 
> >> 
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> >> 
> >> 
> > 
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> 
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
> 
> 
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