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Performance #2626
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On my side I've made some profiling: most of the time is spent in this for loop, it takes ~0.2s per organism on my test setup => ~10sec for 40 orgs => you can easily hit a timeout if you have many orgs |
@hexylena I took the liberty to dockerize your code there: https://github.com/galaxy-genome-annotation/apolpi |
Ahhh awesome @abretaud that'll make it easier to deploy. yeah license is fine :) (Normally I'd do agpl3 to force folks to contribute back their changes, but, in this case I don't think it matters) |
Cool thanks, used on apololo.genouest.org and bipaa.genouest.org/apollo now |
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Yep I noticed it's slow too but I don't know why, maybe it's doing things on the data dir!? |
It's odd, the API responds quickly, it was just through the UI. Anyway |
@abretaud and I are working to debug an issue where the slowness of findAllOrganisms (>30s) is killing the training we're giving.
This route should be fast. like <2 seconds fast. I've replaced it with a flask app that talks directly to the DB and does all of the joins and filtering on the DB side which seems to be MUCH more efficient.
Here's the flask app which just replaces that one route.
I'm running this service and we're just proxying that one route through our own version:
I think there are a couple parts to the issue:
A key point for me is that I really don't think apollo needs a graph database. I think it just needs some time spent understanding how to most effectively use SQL (I'm happy to offer my expertise there.)
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