Add paging to ontomatch service

cmungall commented 7 years ago

The route '/ontolomatch/MP/HP' should return a set of best matches in MP for HP (note this is less than the full all-by-all table).

Currently this gives a gateway timeout. Paging should be added.

Also, we should have a version that works for a specific ID, @drseb would use this.

drseb commented 7 years ago

I would also be happy with the full all-by-all table. How could I obtain this?

julesjacobsen commented 7 years ago

You should be able to just use the API directly:

BMKnowledgeBase bmKnowledgeBase = BMKnowledgeBase.owlLoader()...createKnowledgeBase();
ClassMatcher classMatcher= new ClassMatcher(bmKnowledgeBase);
List<SimpleClassMatch> matches =  classMatcher.matchOntologies("HP", "MP");

jnguyenx commented 7 years ago

We had a look with Chris, it doesn't seem to be an issue with the returned data being too large. But the service takes too long to return anyway, Chris will take a look at that.

cmungall commented 7 years ago

OK, great. To summarize:

for all by all, @drseb can use the java API directly
we can consider having a report exported somewhere, but I'd rather avoid this, see below
I'd still like this to be available as a service. We have a separate ticket to do a service query for any given class: #72
It should actually not be too hard to do all by all as a service. We just calculate this on initialization, possibly caching, driven by what is in the yaml. E.g. the yaml may say calculate all by all for {HP,MP,WBPhenotype,...}. (if you query a combo that is not in the yaml then you are out of luck). Given this is a bit fiddly and that other routes are available, I may classify this as 'nice to have' and punt until afterwards.

drseb commented 7 years ago

I am happy with using the API. I am not closing, because the ticket is about something else now.

monarch-initiative / owlsim-v3

Add paging to ontomatch service #69