[InterMine Dev] Items xml specification suggestion

JD Wong jdmswong at gmail.com
Wed Sep 14 22:01:25 BST 2011


Hi, I have a suggestion for a change to the items XML specifications.
 Currently we are not allowed to have null values as field values.

For example this is allowed:

<item id="2_1" class="Gene">
     <attribute name="primaryIdentifier" value="CG42703"/>
      <attribute name="symbol" value="CG42703"/>
      <attribute name="FlyBaseFeatureType" value="protein_coding_gene"/>
      <attribute name="FlyBaseAnnotationSymbol" value="CG42703"/>
      <attribute name="FlyBaseID" value="FBgn0038156"/>
      <attribute name="FlyBaseCytogenicMap" value="59C4-59C4"/>
</item>

but not this:

<item id="2_1" class="Gene">
     <attribute name="primaryIdentifier" value="CG42703"/>
      <attribute name="symbol" value="CG42703"/>
      <attribute name="FlyBaseFeatureType" value="protein_coding_gene"/>
      <attribute name="FlyBaseAnnotationSymbol" value="CG42703"/>
      <attribute name="FlyBaseID" *value=""/>*
      <attribute name="FlyBaseCytogenicMap" value="59C4-59C4"/>
</item>
this elongates any code we write that produces items XML files, since we
have to include a null contingency for each field, which takes extra time
and troubleshooting.  Is there any way the intermine parser can just know
not to include FlyBaseID when presented with a null value instead of
returning with an error (regarding this example)?

Cheers,
-JD
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