[InterMine Dev] Adding SNP Location

Vallejos, Andrew avallejos at mcw.edu
Mon Aug 17 21:55:14 BST 2009


 

I am trying to add a Location to a SNP object.  

 

Here is an except from dbSNP.pl

 

            if(@alleles == 2) {

                my $snp_item = make_item('SNP');

                $snp_item->set('name', $vf->variation_name);

                $snp_item->set('allele1', $alleles[0]);

                $snp_item->set('allele2', $alleles[1]);

                my $location_item = make_item("Location");

                $location_item->set('start', $vf->start);

                $location_item->set('end', $vf->end);

                #$location_item->set('chromosome', $chromosome_item);

                $location_item->as_xml($writer);

                $snp_item->set('location', $location_item);

                

 

As you can see I create a SNP and a Location.  I then set the location
to the snp.  The database builds correctly.  Integration loads the data
into the tgt database fine.  But then the integration fails with the
following error.

 

 

 

Caused by: org.intermine.objectstore.ObjectStoreException:
org.intermine.metadata.MetaDataException: Reference n

ot found in model: [interface org.intermine.model.bio.SNP].location

        at
org.intermine.objectstore.translating.ObjectStoreTranslatingImpl.execute
(ObjectStoreTranslatingImpl.j

ava:170)

        at
org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForT
ranslatorImpl.execute(ObjectS

toreFastCollectionsForTranslatorImpl.java:191)

        at
org.intermine.objectstore.query.Results.fetchBatchFromObjectStore(Result
s.java:315)

        at
org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManage
r.java:231)

        at
org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManage
r.java:136)

        at
org.intermine.objectstore.query.Results.getBatch(Results.java:290)

        at
org.intermine.objectstore.query.Results.getRowsFromBatch(Results.java:26
8)

        at
org.intermine.objectstore.query.Results.range(Results.java:202)

        at
org.intermine.objectstore.query.SingletonResults.range(SingletonResults.
java:51)

        at org.intermine.objectstore.query.Results.get(Results.java:361)

        ... 35 more

Caused by: org.intermine.metadata.MetaDataException: Reference not found
in model: [interface org.intermine.mode

l.bio.SNP].location

        at
org.intermine.dataconversion.ItemToObjectTranslator.translateFromDbObjec
t(ItemToObjectTranslator.java

:353)

        at
org.intermine.objectstore.translating.ObjectStoreTranslatingImpl.execute
(ObjectStoreTranslatingImpl.j

ava:157)

        ... 44 more

 

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

avallejos at mcw.edu

 

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