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

[Richard Holland]

Could do.

On 11 Mar 2010, at 11:14, mark.schreiber at novartis.com wrote:

> 
> 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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> > >>    <mailto:Biojava-l at lists.open-bio.org>
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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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> 
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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/