[InterMine Dev] Items xml specification suggestion

Alex Kalderimis alex at flymine.org
Thu Sep 15 15:40:42 BST 2011


When I raised this question myself the current practice was described as
favouring explicitness over concision - files should not by this
reckoning mistakenly contain gaps in the information due to oversights. 

I could add a flag to the Perl modules that would cause empty field
values to not be written, so that would give you that functionality on
request if you needed it.

Alex Kalderimis

On Wed, 2011-09-14 at 17:01 -0400, 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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> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

-- 
Alex Kalderimis
Software Developer
InterMine
Cambridge Systems Biology Centre
Tennis Court Road - CB2 1QR
University of Cambridge
ajk59 at cam.ac.uk




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