[InterMine Dev] Adding SNP Location

Vallejos, Andrew avallejos at mcw.edu
Tue Aug 18 15:10:57 BST 2009


  <class name="SNP" extends="PointMutation" is-interface="true">
    <attribute name="chromosomeStart" type="java.lang.String"/>
    <attribute name="allele2" type="java.lang.String"/>
    <attribute name="snp" type="java.lang.String"/>
    <attribute name="allele1" type="java.lang.String"/>
    <attribute name="chromosomeEnd" type="java.lang.String"/>
    <collection name="consequenceTypes"
referenced-type="ConsequenceType"/>
    <collection name="validations" referenced-type="ValidationState"/>
    <collection name="sources" referenced-type="Source"/>
  </class>

-----Original Message-----
From: Richard Smith [mailto:richard at flymine.org] 
Sent: Tuesday, August 18, 2009 8:59 AM
To: Vallejos, Andrew
Cc: Julie Sullivan; dev at intermine.org
Subject: Re: [InterMine Dev] Adding SNP Location

Right, the chromosome reference needs to be removed (as you discovered)
because the SNP class is merging with SNP from so_additions.xml, which
is an extension (via a few classes) of LocatedSequenceFeature.

This means it has a chromosome reference and a chromosomeLocation
reference.  You should set both of these in the snp source.

So the location reference isn't needed but it would be interesting to
find out why it is causing an error.  Could you send the definition of
the SNP class that appears in the merged model XML, run:

   xmllint --format ratmine/dbmodel/build/model/genomic_model.xml

Also could you send the result of '\d snp' in the production database.

Cheers,
Richard.




Vallejos, Andrew wrote:
> 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
> 
> 
> 
> _______________________________________________
> dev mailing list
> dev at mail.intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
> 




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