Allow getting multiple GOTerms at Once

Question

Allow getting multiple GOTerms at Once

Opened this issue 8 years ago · 4 comments

Currently have to make many 'getitem' calls to get a list of many terms (such as for enrichment computation). This introduces significant slowdown to other wise near instant functions (such as enrichment).

Answer 1 · 2016-12-27T05:17:21.000Z

Can't we put an lru cache on this?

…

On Mon, Dec 26, 2016, 7:53 PM Joe Jeffers ***@***.***> wrote: Currently have to make many '*getitem*' calls to get a list of many terms (such as for enrichment computation). This introduces significant slowdown to other wise near instant functions (such as enrichment). — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#46>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACcpvwkJPH9OcFu40RxC1G_6vQlHk-HRks5rMG-hgaJpZM4LV-aX> .

Answer 2 · 2016-12-27T16:24:54.000Z

There is already, and it does help with subsequent requests, but it doesn't help with the first requests. It's not a huge deal. I was able to get the actual enrichment computation down to almost trivial, and I have a couple other optimizations in mind, so it should be under 20 seconds for any normal query now, which won't cause me to lose sleep if we publicize the server. Though it is still somewhat accidental DDoS prone.

Answer 3 · 2016-12-28T22:55:09.000Z

BTW, Are you using the built in enrichment function inside of the Ontology object? That one should be pretty fast.

Answer 4 · 2016-12-28T23:00:49.000Z

I did and actually did some tweaks to make it faster, but the biggest slowdown is still initially building the objects, it's fine if we dont, just thought I'd bring it up.

…

On Dec 28, 2016 4:55 PM, "Rob Schaefer" ***@***.***> wrote: BTW, Are you using the built in enrichment function inside of the Ontology object? That one should be pretty fast. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#46 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGw_DpZMSSH2XfwF_yd9LnV_ePM3pZ7Qks5rMujNgaJpZM4LV-aX> .