[InterMine Dev] Adding SNP Location

Richard Smith richard at flymine.org
Tue Aug 18 10:30:18 BST 2009


I think SNP should have a 'chromosomeLocation' reference already as it
inherits from LocatedSequenceFeature, so for consistency it would be
better to use that reference.

However, the perl API shouldn't allow you to set a field on an item if
that field isn't in the model.  Is it possible your perl code is
pointing at a different model to that of the production database?

Or there is a bug in intermine/perl/lib/InterMine/Item.pm.

Cheers,
Richard.




Julie Sullivan wrote:
> Andrew,
> 
> This looks to be the interesting bit of the stacktrace:
> 
>> Reference not found in model: [interface 
>> org.intermine.model.bio.SNP].location
> 
> You need to add a reference to location in SNP.  To do this, add this 
> line to the SNP entry in your snp_additions.xml file:
> 
>      <reference name="location" referenced-type="Location" />   
> 
> Then run ant clean build-db in ratmine/dbmodel to update the model.  
> Here is some documentation about the additions file:
> 
>     http://intermine.org/wiki/ModelMerging
> 
> 
> 
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