search

geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
38 stars 12 forks source link

Autocomplete issues in Noctua #411

Closed cmungall closed 7 years ago

cmungall commented 7 years ago

@dosumis says: https://github.com/geneontology/go-ontology/issues/13150#issuecomment-293315764

I’ve been noticing general flakiness in GO term autocomplete this afternoon. Was halfway through writing a bug report when it fixed itself. Autocomplete on all other OBO terms seems to be working fine.

@BarbaraCzub says:

https://github.com/geneontology/go-ontology/issues/13150#issuecomment-293321257

Unfortunately my autocomplete issues have not resolved themselves. In fact new ones (which can be seen in the same Nactua model 'SynGO no. 1c') have emerged since I sent the last message.

@BarbaraCzub, I don't have sufficient info to replicate this. Can you give more details? Is the problem lag, or that the term does not exist?

kltm commented 7 years ago

As it stands now, Noctua is unusable as no ontology autocomplete actually returns anything useful. As the servers are responding, the issue would be the load. The loads were successful, so we need to dig into the data.

cmungall commented 7 years ago

It may be an issue with loads

This seems fine: http://noctua-amigo.berkeleybop.org/amigo/load_details

However, this is not so good: http://noctua-amigo.berkeleybop.org/amigo/search/ontology

One hypothesis is clobbering, but it should not be possible to clobber a whole ontology, and I believe owltools should load everything together in memory to begin with.

cmungall commented 7 years ago

Hmm, http://noctua-amigo.berkeleybop.org/amigo/load_details

has this:

2017-04-10 2017-04-10 http://purl.obolibrary.org/obo/extensions/go-plus.owl

but this is an incorrect URL (which returns S3 XML which unfortunately the OWLAPI treats as an empty ontology)

I filed this https://github.com/owlcs/owlapi/issues/657

But it may not be directly related. It may be that gave the wrong IRI in go-plus which causes issues with imports

kltm commented 7 years ago

@BarbaraCzub I believe that Noctua autocomplete should now be working as expected and with the expected terms in place (when I tested).

@cmungall For future reference, could you give a little detail about the exact nature of the error?

cmungall commented 7 years ago

Thanks Seth!

Just to be clear, I was not reporting an error myself, I was transferring the information from the ontology tracker. I provided all the info I had.

BarbaraCzub commented 7 years ago

Hi @kltm and @cmungall

Thank you for resolving the autocomplete issue. I have just checked my models and all the terms that were previously displayed as the GO term ID, are now displayed as GO term name. So this fix appears to have worked. Thanks!

Barbara