[InterMine Dev] cannot create templates taking lists

Jun Zhao jun.zhao at zoo.ox.ac.uk
Fri Nov 20 12:46:39 GMT 2009

Hi Richard,

Richard Smith wrote:
> Hi Jun,
> Thanks very much for your comments, some responses below:

Thank you very much for your very helpful response:)
>> I was experimenting with embedding Templates from FlyMine in my web 
>> pages. The templates taking one parameter worked very well for me. 
>> However, as the warning messages shown to me, the Embed function does 
>> not work when the templates take lists as inputs.
> This is true, the embedding of templates doesn't currently work with
> lists.  However, there is a workaround as most templates that accept
> identifiers use LOOKUP constraints with which you can use a comma
> separated list of identifiers.

Yes, this does work for me now:)

However, is there a way for me to control how the results are ordered in 
the template? For example, when embedding this template as a widget in 
my query application, it would be nice if I can sort the results by the 
order of the query input. Simply ordering results by the primary gene 
identifiers wouldn't help my users to figure out which query genes have 
been returned with information by the flymine widget.

If I can't do this, I will use the web service instead.

>> I am curious to know what the near plan for supporting lists.
> We do plan to add support for uploading lists via the web service and
> for authenticating so users can access saved information from their
> MyMine account.  We have done some work on these and hope to have
> time to do more in the next few months.

This is great! It can save my development effort too. But again, a 
flexibility to order the results returned by the service is very 
important for my application.
> We will also look into fetching data about individual genes, proteins,
> etc via a RESTful interface.

Looking forward to this!:)
>> Meanwhile, during the process of using the web services, I also noticed 
>> that the performance varied very much. Sometimes it took a very long 
>> time to return results containng only one record. I guess it is not the 
>> size of the results that matters, but the complexity of the query?
> You are right it is down to the complexity of the query, not the number
> of rows.  But if you are running templates from FlyMine they should be
> precomputed and run quickly.  If you have some examples of queries that
> are consistently slow we can look into it.

I will keep an eye on this. The template I was working with this morning 
performed consistent very well. It's the template retrieving Orthologues 
and GO annotations for D. melanogaster genes.



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