[InterMine Dev] Adding SNP Location

Vallejos, Andrew avallejos at mcw.edu
Tue Aug 18 16:16:10 BST 2009


I have not added a Location object to the additions file.  I assumed
that the location object was inherited. 

-----Original Message-----
From: Richard Smith [mailto:richard at flymine.org] 
Sent: Tuesday, August 18, 2009 10:09 AM
To: Vallejos, Andrew
Cc: Julie Sullivan; dev at intermine.org
Subject: Re: [InterMine Dev] Adding SNP Location

Hmmm, so it looks like the location reference hasn't made it to the
merged model.  If you change _additions.xml files the changes don't
take effect until you do an 'ant clean build-db' in the dbmodel
directory.  I think that explains the error.

I should have pointed out before that you could remove chromosomeStart
and chromosomeEnd from SNP now the coordinates are moved to the
Location class.

Cheers,
Richard.



Vallejos, Andrew wrote:
>   <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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