[InterMine Dev] Items xml specification suggestion

Richard Smith richard at flymine.org
Thu Sep 15 16:33:39 BST 2011


Hi JD,
I notice that the names of attributes you're using are quite different
to the ones we use in FlyMine and the convention followed by the other
MODs.  I know you're just at the initial testing stage but it might
be worth looking at what we've already done in FlyMine.

Cheers,
Richard.


On 14/09/2011 22:01, JD Wong wrote:
> 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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