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

[Richard Holland]

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 like a 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/