[InterMine Dev] Adding SNP Location

Vallejos, Andrew avallejos at mcw.edu
Tue Aug 18 14:30:25 BST 2009


The modified SNP additions file. 

As you can see I already have a location reference field.  I had to
comment out the chromosome reference because it was causing an error.

<?xml version="1.0"?>
<classes>
   <class name="SNP" is-interface="true">
     <attribute name="chromosomeStart" type="java.lang.String"/>
     <attribute name="chromosomeEnd" type="java.lang.String"/>
     <attribute name="snp" type="java.lang.String"/>
     <attribute name="allele1" type="java.lang.String"/>
     <attribute name="allele2" type="java.lang.String"/>
 <!--    <reference name="chromosome" referenced-type="Chromosome"/> -->
		 <reference name="location" referenced-type="Location"
/>
     <collection name="validations" referenced-type="ValidationState" />
     <collection name="consequenceTypes"
referenced-type="ConsequenceType"/>
    <collection name="sources" referenced-type="Source"/>
   </class>

   <class name="ValidationState" is-interface="true">
     <attribute name="state" type="java.lang.String"/>
   </class>

   <class name="ConsequenceType" is-interface="true">
     <attribute name="type" type="java.lang.String"/>
   </class>

  <class name="Source" is-interface="true">
     <attribute name="source" type="java.lang.String"/>
   </class>
</classes>


-----Original Message-----
From: Julie Sullivan [mailto:julie at flymine.org] 
Sent: Tuesday, August 18, 2009 3:46 AM
To: Vallejos, Andrew
Cc: dev at intermine.org
Subject: Re: [InterMine Dev] Adding SNP Location

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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