path query question and region search startup

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

path query question and region search startup

joe carlson
Hi,

I’ve looked through the code and I see that there is code for aggregate functions (like count, max, min,…). How can these be accessed through a path query? I can’t seem to figure this out.

Also, I’m about to open a feature request in the issue list. The startup time for the genomic region search is very long in our mine because of the 500K scaffolds that we have in the db. (and it’s about to get the wheat genome added with another huge number of scaffolds.)

I can make the region startup better by setting the batch size in GenomicRegionSearchQueryRunner (and initial size in the chrInfoList) to something more appropriate for us. Can this be made a configurable property?

Can you suggest other things that may speed up this startup?

Thanks,

Joe Carlson
_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: path query question and region search startup

Julie Sullivan


On 08/12/14 05:40, Joe Carlson wrote:
> Hi,
>
> I’ve looked through the code and I see that there is code for aggregate functions (like count, max, min,…). How can these be accessed through a path query? I can’t seem to figure this out.

That hasn't been implemented yet, but it high on the priority list.

> Also, I’m about to open a feature request in the issue list. The startup time for the genomic region search is very long in our mine because of the 500K scaffolds that we have in the db. (and it’s about to get the wheat genome added with another huge number of

scaffolds.)

> I can make the region startup better by setting the batch size in GenomicRegionSearchQueryRunner (and initial size in the chrInfoList) to something more appropriate for us. Can this be made a configurable property?

Thanks!

> Can you suggest other things that may speed up this startup?

I'll take a look. And hopefully some of the speed improvements we've
made for the next InterMine release will help too. (InterMine 1.4 should
be ready for Xmas.)

> Thanks,
>
> Joe Carlson
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev