[InterMine Dev] source_keys.properties file not read

Julie Sullivan julie at flymine.org
Thu Sep 8 09:56:04 BST 2011

Hi Thomas

Your keys and additions files look correct to me.

Is that the only source you are running?  The keys in that file are integration 
keys, they aren't used when loading a single source.  The build system uses the 
fields listed in that file to merge objects created in that source with objects 
already stored in the database, the file is not used when loading new objects. 
If you need unique objects in a single source, you'll have to do that in the 
converter.  Here's some more information on the keys file:


Also, try naming each key, eg. instead of DataSet.key use DataSet.key_name 
(which is the same name used by other sources).  This is the name of the index 
used by postgres, it's a good idea to have the same name for each across sources 
so you don't end up with duplicates.

Let me know if that doesn't solve your problem.


On 07/09/11 23:34, Thomas TRIPLET wrote:
> Hello,
> I've created a data source for the Enzyme Nomenclature, which works fine,
> except that I am getting duplicates in the database (same EC number). I did
> define a key in the keys.properties file though, but it is as if the file
> wasn't parsed at all.
> The additions.xml file contains the following:
> <classes>
> <class name="EnzymeClassification" is-interface="true">
>   <attribute name="ecNumber" type="java.lang.String"/>
>   <attribute name="acceptedName" type="java.lang.String"/>
>   <attribute name="systematicName" type="java.lang.String"/>
>   <attribute name="description" type="java.lang.String"/>
>   <attribute name="isObsolete" type="boolean"/>
>   <reference name="parentNode" referenced-type="EnzymeClassification"/>
>   <collection name="dataSets" referenced-type="DataSet" />
>   </class>
> </classes>
> In the keys.properties, I have
> DataSet.key = name
> EnzymeClassification.key = ecNumber
> EnzymeClassification.key_name = acceptedName
> Am I missing something or is there a way to force the keys definitions to be
> read?
> Thanks
> Thomas
> --
> Thomas Triplet, Ph.D.
> http://www.thomastriplet.net
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